diff --git a/client/galaxy/scripts/components/PluginList.vue b/client/galaxy/scripts/components/PluginList.vue
index 2f70becf0c7..cf88c5c2d7e 100644
--- a/client/galaxy/scripts/components/PluginList.vue
+++ b/client/galaxy/scripts/components/PluginList.vue
@@ -16,19 +16,24 @@
                 <table v-if="match(plugin)">
                     <tr class="ui-thumbnails-item" @click="select(plugin)">
                         <td>
-                            <img v-if="plugin.logo" alt="ui thumbnails" class="ui-thumbnails-image" :src="plugin.logo" />
+                            <img
+                                v-if="plugin.logo"
+                                alt="ui thumbnails"
+                                class="ui-thumbnails-image"
+                                :src="plugin.logo"
+                            />
                             <div v-else class="ui-thumbnails-icon fa fa-eye" />
                         </td>
                         <td>
-                            <div class="ui-thumbnails-title font-weight-bold text-dark">{{ plugin.html }}</div>
-                            <div class="ui-thumbnails-text text-dark">{{ plugin.description }}</div>
+                            <div class="ui-thumbnails-title font-weight-bold">{{ plugin.html }}</div>
+                            <div class="ui-thumbnails-text">{{ plugin.description }}</div>
                         </td>
                     </tr>
                     <tr v-if="!fixed">
                         <td />
                         <td v-if="plugin.name == name">
                             <div v-if="hdas && hdas.length > 0">
-                                <div class="font-weight-bold text-dark">Select a dataset to visualize:</div>
+                                <div class="font-weight-bold">Select a dataset to visualize:</div>
                                 <div class="ui-select">
                                     <select class="select" v-model="selected">
                                         <option v-for="file in hdas" :key="file.id" :value="file.id">{{
diff --git a/client/galaxy/scripts/components/Tags/model.js b/client/galaxy/scripts/components/Tags/model.js
index 821c1c0c009..de079521a94 100644
--- a/client/galaxy/scripts/components/Tags/model.js
+++ b/client/galaxy/scripts/components/Tags/model.js
@@ -51,7 +51,6 @@ function TagModel(props = {}) {
         get: function() {
             if (!this.text.length) return false;
             return this.text != "name:";
-
         }
     });
 }
diff --git a/client/galaxy/scripts/components/Toolshed/InstallationSettings.vue b/client/galaxy/scripts/components/Toolshed/InstallationSettings.vue
index 41673819f71..11c1b0c4cae 100644
--- a/client/galaxy/scripts/components/Toolshed/InstallationSettings.vue
+++ b/client/galaxy/scripts/components/Toolshed/InstallationSettings.vue
@@ -84,7 +84,7 @@ export default {
     },
     methods: {
         findSection: function(name) {
-            const result = ['', ''];
+            const result = ["", ""];
             if (name) {
                 const found = this.toolSections.find(s => {
                     return s.name.toLowerCase().trim() == name.toLowerCase().trim();
diff --git a/client/galaxy/scripts/components/Toolshed/RepositoryDetails.vue b/client/galaxy/scripts/components/Toolshed/RepositoryDetails.vue
index a79d9216d5e..4a3eee8ed31 100644
--- a/client/galaxy/scripts/components/Toolshed/RepositoryDetails.vue
+++ b/client/galaxy/scripts/components/Toolshed/RepositoryDetails.vue
@@ -157,7 +157,9 @@ export default {
         },
         setupRepository: function(details) {
             this.selectedChangeset = details.changeset_revision;
-            this.selectedRequiresPanel = details.includes_tools_for_display_in_tool_panel || details.repository.type == "repository_suite_definition";
+            this.selectedRequiresPanel =
+                details.includes_tools_for_display_in_tool_panel ||
+                details.repository.type == "repository_suite_definition";
             this.showSettings = true;
         },
         uninstallRepository: function(details) {
diff --git a/client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue b/client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue
index 55cbf0ed008..4e9e9a3869f 100644
--- a/client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue
+++ b/client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue
@@ -4,8 +4,7 @@
             <h2 id="data-managers-title">Local Data</h2>
             <p>
                 Data Managers are used to manage Galaxy's local data. They can be installed manually, or via the
-                <b-link :href="toolShedLink" target="galaxy_main">ToolShed</b-link>. For more
-                comprehensive information
+                <b-link :href="toolShedLink" target="galaxy_main">ToolShed</b-link>. For more comprehensive information
                 <b-link href="https://galaxyproject.org/admin/tools/data-managers/" target="_blank">See the Wiki</b-link
                 >.
             </p>
@@ -17,10 +16,10 @@
 import { getAppRoot } from "onload/loadConfig";
 
 export default {
-    computed:{
+    computed: {
         toolShedLink() {
-            return `${getAppRoot()}admin_toolshed/browse_tool_sheds`
+            return `${getAppRoot()}admin_toolshed/browse_tool_sheds`;
         }
     }
-}
+};
 </script>
diff --git a/client/galaxy/scripts/components/login/Register.vue b/client/galaxy/scripts/components/login/Register.vue
index 588e2251ec9..30a90483ce8 100644
--- a/client/galaxy/scripts/components/login/Register.vue
+++ b/client/galaxy/scripts/components/login/Register.vue
@@ -27,7 +27,10 @@
                                     ('.', '_', '-').</b-form-text
                                 >
                             </b-form-group>
-                            <b-form-group v-if="mailing_join_addr && server_mail_configured" label="Subscribe to mailing list">
+                            <b-form-group
+                                v-if="mailing_join_addr && server_mail_configured"
+                                label="Subscribe to mailing list"
+                            >
                                 <input name="subscribe" type="checkbox" v-model="subscribe" />
                             </b-form-group>
                             <b-button name="create" type="submit" :disabled="disableCreate">Create</b-button>
diff --git a/client/galaxy/scripts/components/xrefs.vue b/client/galaxy/scripts/components/xrefs.vue
index 13c005243ba..97c0529bdd1 100644
--- a/client/galaxy/scripts/components/xrefs.vue
+++ b/client/galaxy/scripts/components/xrefs.vue
@@ -5,10 +5,10 @@
         </h4>
         <table>
             <tr v-for="(xref, index) in xrefs" v-bind:key="index">
-                <th> - {{xref.reftype}}: </th>
+                <th>- {{ xref.reftype }}:</th>
                 <td>
                     <template v-if="xref.reftype == 'bio.tools'">
-                        <a :href="`https://bio.tools/${xref.value}`" target="_blank">{{xref.value}}</a>
+                        <a :href="`https://bio.tools/${xref.value}`" target="_blank">{{ xref.value }}</a>
                     </template>
                     <template v-else>
                         {{ xref.value }}
diff --git a/client/galaxy/scripts/entry/panels/tool-panel.js b/client/galaxy/scripts/entry/panels/tool-panel.js
index 47b1ab4cfbe..e59bb4f492e 100644
--- a/client/galaxy/scripts/entry/panels/tool-panel.js
+++ b/client/galaxy/scripts/entry/panels/tool-panel.js
@@ -52,9 +52,17 @@ const ToolPanel = Backbone.View.extend({
                 title: _l("Show favorites"),
                 icon: "fa fa-star-o",
                 onclick: e => {
-                    $("#tool-search-query")
-                        .val("#favorites")
-                        .trigger("change");
+                    const $search_query = $("#tool-search-query");
+                    const $header_btn = $(".panel-header-button");
+                    $header_btn.find(".fa").toggleClass("fa-star-o fa-star");
+                    $header_btn.tooltip("hide");
+                    if ($search_query.val().indexOf("#favorites") != -1) {
+                        $search_query.val("");
+                        $search_query.keyup();
+                        $header_btn.attr("title", "");
+                    } else {
+                        $search_query.val("#favorites").trigger("change");
+                    }
                 }
             });
             panel_buttons.push(this.favorite_button);
diff --git a/client/galaxy/scripts/layout/page.js b/client/galaxy/scripts/layout/page.js
index af6b5c2ee99..bc7ccbf3462 100644
--- a/client/galaxy/scripts/layout/page.js
+++ b/client/galaxy/scripts/layout/page.js
@@ -172,8 +172,8 @@ const View = Backbone.View.extend({
             `<div id="everything">
                 <div id="background"/>
                 <div id="masthead"/>
-                <div id="messagebox"/>
-                <div id="inactivebox" class="panel-warning-message" />
+                <div id="messagebox" class="full-message"/>
+                <div id="inactivebox" class="full-message panel-warning-message" />
                 <div id="columns">
                     <div id="left" class="unified-panel"/>
                     <div id="center" />
diff --git a/client/galaxy/scripts/mvc/history/multi-panel.js b/client/galaxy/scripts/mvc/history/multi-panel.js
index 276ec095870..7896475eaf8 100644
--- a/client/galaxy/scripts/mvc/history/multi-panel.js
+++ b/client/galaxy/scripts/mvc/history/multi-panel.js
@@ -95,7 +95,6 @@ var HistoryViewColumn = Backbone.View.extend(baseMVC.LoggableMixin).extend({
             return false;
         }
         return columnLeft <= viewRight;
-
     },
 
     /** shortcut to the panel */
diff --git a/client/galaxy/scripts/mvc/library/library-folderlist-view.js b/client/galaxy/scripts/mvc/library/library-folderlist-view.js
index 4c272c2e1a7..7ad83bd255f 100644
--- a/client/galaxy/scripts/mvc/library/library-folderlist-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folderlist-view.js
@@ -355,8 +355,8 @@ var FolderListView = Backbone.View.extend({
 
     renderSortIcon: function() {
         $('[class*="sort-icon"]')
-        .removeClass("fa-sort-alpha-desc")
-        .removeClass("fa-sort-alpha-asc");
+            .removeClass("fa-sort-alpha-desc")
+            .removeClass("fa-sort-alpha-asc");
 
         if (this.current_sort_order === "asc") {
             $(`.sort-icon-${this.current_sort_key}`).addClass("fa-sort-alpha-asc");
diff --git a/client/galaxy/scripts/mvc/library/library-model.js b/client/galaxy/scripts/mvc/library/library-model.js
index 6ad5f054bde..b8b0a4ea24b 100644
--- a/client/galaxy/scripts/mvc/library/library-model.js
+++ b/client/galaxy/scripts/mvc/library/library-model.js
@@ -74,7 +74,7 @@ var FolderAsModel = LibraryItem.extend({
 });
 
 var Folder = Backbone.Collection.extend({
-    model: LibraryItem,
+    model: LibraryItem
 });
 
 var FolderContainer = Backbone.Model.extend({
diff --git a/client/galaxy/scripts/mvc/library/library-util.js b/client/galaxy/scripts/mvc/library/library-util.js
index bb174a7cb56..ab330d9925d 100644
--- a/client/galaxy/scripts/mvc/library/library-util.js
+++ b/client/galaxy/scripts/mvc/library/library-util.js
@@ -18,14 +18,12 @@ var generateComparator = (sort_key, sort_order) => (itemA, itemB) => {
     if (typeof itemA.get(sort_key) === "number") {
         comparable_itemA_key = itemA.get(sort_key);
         comparable_itemB_key = itemB.get(sort_key);
-    }
-    else
-    {
+    } else {
         comparable_itemA_key = itemA.get(sort_key).toLowerCase();
         comparable_itemB_key = itemB.get(sort_key).toLowerCase();
     }
 
-    if ( comparable_itemA_key > comparable_itemB_key) {
+    if (comparable_itemA_key > comparable_itemB_key) {
         return sort_order === "asc" ? 1 : -1;
     }
     if (comparable_itemB_key > comparable_itemA_key) {
diff --git a/client/galaxy/scripts/mvc/tag.js b/client/galaxy/scripts/mvc/tag.js
index 9cf9c119a70..6e9ad498d88 100644
--- a/client/galaxy/scripts/mvc/tag.js
+++ b/client/galaxy/scripts/mvc/tag.js
@@ -117,7 +117,9 @@ var TagsEditor = Backbone.View.extend(baseMVC.LoggableMixin)
             });
             if (renderedArray.length === 0) {
                 // If there are no tags to render we just show the add-tag-button
-                renderedArray.push(`<img alt="add tag button" src=${addButton} class="add-tag-button" title="Add tags"/>`);
+                renderedArray.push(
+                    `<img alt="add tag button" src=${addButton} class="add-tag-button" title="Add tags"/>`
+                );
             }
             return renderedArray.join(" ");
         },
diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js
index ba499e4d9b9..7b99a9abea6 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-base.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js
@@ -280,13 +280,13 @@ export default FormBase.extend({
                 }
             }).$mount(vm);
         }
-	if (options.xrefs && options.xrefs.length) {
+        if (options.xrefs && options.xrefs.length) {
             var xrefInstance = Vue.extend(xrefs);
             vm = document.createElement("div");
             $el.append(vm);
             new xrefInstance({
                 propsData: {
-                    id: options.id, 
+                    id: options.id,
                     source: "tools"
                 }
             }).$mount(vm);
diff --git a/client/galaxy/scripts/mvc/ui/ui-select-content.js b/client/galaxy/scripts/mvc/ui/ui-select-content.js
index d9baa250c59..27f5de24554 100644
--- a/client/galaxy/scripts/mvc/ui/ui-select-content.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select-content.js
@@ -335,7 +335,7 @@ const View = Backbone.View.extend({
         this.button_type = new Ui.RadioButton.View({
             value: this.model.get("current"),
             data: this.button_data,
-            cls: "mr-2",
+            cls: "pr-lg-2",
             onchange: function(value) {
                 self.model.set("current", value);
                 self.trigger("change");
@@ -346,7 +346,6 @@ const View = Backbone.View.extend({
         this.button_dialog = new Ui.Button({
             icon: "fa-folder-open-o",
             tooltip: "Browse Datasets",
-            cls: "ml-2",
             onclick: () => {
                 const current = this.model.get("current");
                 const cnf = this.config[current];
@@ -364,10 +363,10 @@ const View = Backbone.View.extend({
         });
 
         // append views
-        const $fields = $("<div/>").addClass("w-100");
+        const $fields = $("<div/>").addClass("overflow-auto w-100 py-2 py-lg-0 pr-lg-2 ");
         this.$el
             .empty()
-            .addClass("d-flex flex-row")
+            .addClass("d-flex flex-row flex-wrap flex-lg-nowrap")
             .append($("<div/>").append(this.button_type.$el))
             .append($fields)
             .append($("<div/>").append(this.button_dialog.$el));
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-canvas.js b/client/galaxy/scripts/mvc/workflow/workflow-canvas.js
index 9ea70d5e101..5825aa23b47 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-canvas.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-canvas.js
@@ -97,7 +97,7 @@ class CanvasManager {
         this.init_copy_paste();
     }
     setZoom(zoomLevel) {
-        this.zoomLevel = Math.min(Math.max(0, zoomLevel), zoomLevels.length-1);
+        this.zoomLevel = Math.min(Math.max(0, zoomLevel), zoomLevels.length - 1);
         this.canvasZoom = zoomLevels[this.zoomLevel];
         // Set CSS transform to appropriate zoom level
         this.cv.css("transform-origin", "top left");
@@ -115,26 +115,28 @@ class CanvasManager {
             bottom: "1rem",
             cursor: "pointer"
         });
-        const zoomButton = $(`<a class="btn btn-light" title="Reset Zoom Level">${zoomLevels[defaultZoomLevel] * 100}%</a>`).css({
+        const zoomButton = $(
+            `<a class="btn btn-light" title="Reset Zoom Level">${zoomLevels[defaultZoomLevel] * 100}%</a>`
+        ).css({
             width: "4rem"
         });
 
         zoomControl.append(
             $('<a class="btn btn-secondary fa fa-minus"/>').click(() => {
                 this.setZoom(this.zoomLevel - 1);
-                zoomButton.text(Math.floor(zoomLevels[this.zoomLevel] * 100) + '%');
+                zoomButton.text(Math.floor(zoomLevels[this.zoomLevel] * 100) + "%");
             })
         );
         zoomControl.append(
             zoomButton.click(() => {
                 this.setZoom(defaultZoomLevel);
-                zoomButton.text(Math.floor(zoomLevels[this.zoomLevel] * 100) + '%');
+                zoomButton.text(Math.floor(zoomLevels[this.zoomLevel] * 100) + "%");
             })
         );
         zoomControl.append(
             $('<a class="btn btn-secondary fa fa-plus"/>').click(() => {
                 this.setZoom(this.zoomLevel + 1);
-                zoomButton.text(Math.floor(zoomLevels[this.zoomLevel] * 100) + '%');
+                zoomButton.text(Math.floor(zoomLevels[this.zoomLevel] * 100) + "%");
             })
         );
         this.cv.closest("#workflow-canvas-body").append(zoomControl);
diff --git a/client/galaxy/scripts/mvc/workflow/workflow.js b/client/galaxy/scripts/mvc/workflow/workflow.js
index 9530a6836f1..9359208cbc5 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow.js
@@ -158,12 +158,12 @@ const WorkflowItemView = Backbone.View.extend({
                         <a class="dropdown-item" href="${getAppRoot()}api/workflows/${
                 this.model.id
             }/download?format=json-download">Download</a>
-                        <a class="dropdown-item" id="copy-workflow">Copy</a>
-                        <a class="dropdown-item" id="rename-workflow">Rename</a>
+                        <a class="dropdown-item" href="javascript:void(0)" id="copy-workflow">Copy</a>
+                        <a class="dropdown-item" href="javascript:void(0)" id="rename-workflow">Rename</a>
                         <a class="dropdown-item" href="${getAppRoot()}workflow/display_by_id?id=${
                 this.model.id
             }">View</a>
-                        <a class="dropdown-item" id="delete-workflow">Delete</a>
+                        <a class="dropdown-item" href="javascript:void(0)" id="delete-workflow">Delete</a>
                     </div>`;
         } else {
             return `<div class="dropdown-menu">
@@ -171,7 +171,7 @@ const WorkflowItemView = Backbone.View.extend({
                 "owner"
             )}&slug=${this.model.get("slug")}">View</a>
                         <a class="dropdown-item" href="${getAppRoot()}workflows/run?id=${this.model.id}">Run</a>
-                        <a class="dropdown-item" id="copy-workflow">Copy</a>
+                        <a class="dropdown-item" href="javascript:void(0)" id="copy-workflow">Copy</a>
                         <a class="dropdown-item link-confirm-shared-${
                             this.model.id
                         }" href="${getAppRoot()}workflow/sharing?unshare_me=True&id=${this.model.id}">Remove</a></li>
diff --git a/client/galaxy/scripts/viz/trackster/filters.js b/client/galaxy/scripts/viz/trackster/filters.js
index cb458fe3371..aae4ee876b2 100644
--- a/client/galaxy/scripts/viz/trackster/filters.js
+++ b/client/galaxy/scripts/viz/trackster/filters.js
@@ -323,7 +323,6 @@ _.extend(NumberFilter.prototype, {
      */
     applies_to: function(element) {
         return element.length > this.index;
-
     },
     /**
      * Helper function: returns true if value in in filter's [low, high] range.
diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index de554e1ae58..07dad2de6f0 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -10,19 +10,9 @@
 $fa-font-path: "../../../node_modules/font-awesome/fonts/";
 @import "../../../node_modules/font-awesome/scss/font-awesome.scss";
 
-.fa-icon {
-    // TODO: remove fa-icon and replace with fa
-    @extend .fa;
-}
-
 @import "select2.scss";
 @import "jquery.rating.scss";
 
-/* fix for zero width select2 - remove when fixed there */
-.select2-minwidth {
-    min-width: 256px;
-}
-
 // galaxy sub-components
 @import "reports";
 @import "frame.scss";
@@ -38,7 +28,24 @@ $fa-font-path: "../../../node_modules/font-awesome/fonts/";
 @import "message.scss";
 @import "toolshed.scss";
 
-// Mixins
+// ==== Select2 ====
+/* fix for zero width select2 - remove when fixed there */
+.select2-minwidth {
+    min-width: 256px;
+}
+.select2-drop-active,
+.select2-drop-above.select2-drop-active {
+    border: $border-default;
+    .select2-search {
+        @extend .pt-1;
+    }
+}
+.select2-drop {
+    background: $body-bg;
+    color: $text-color;
+}
+
+// ==== Mixins ====
 @mixin user-select($select) {
     -webkit-touch-callout: #{$select};
     @each $pre in -webkit-, -moz-, -ms-, -o-, -khtml- {
@@ -47,17 +54,6 @@ $fa-font-path: "../../../node_modules/font-awesome/fonts/";
     #{user-select}: #{$select};
 }
 
-.unselectable {
-    @include user-select(none);
-}
-
-.parent-width {
-    //TODO: check out box-sizing w/ bs4
-    //@include box-sizing(border-box);
-    width: 100%;
-    *width: 90%;
-}
-
 @mixin border-radius($radius) {
     // from font-awesome 3.0
     -webkit-border-radius: $radius;
@@ -65,121 +61,117 @@ $fa-font-path: "../../../node_modules/font-awesome/fonts/";
     border-radius: $radius;
 }
 
-// ==== Real (basic) styles ====
+// ==== Basic styles ====
+
+body {
+    @extend .m-2;
+}
+
+.unselectable {
+    @include user-select(none);
+}
+
+.parent-width {
+    @extend .w-100;
+}
 
 .clear {
     @include clearfix();
 }
 
-body {
+// ==== Page layout styles ====
+
+.full-content {
+    @extend .m-0;
+    @extend .p-0;
+    @extend .w-100;
+    @extend .h-100;
+    @extend .overflow-hidden;
+    @extend .position-absolute;
     background: $body-bg;
     color: $text-color;
-    margin: 10px;
+}
 
-    // For panel layout pages
-    &.full-content {
-        overflow: hidden;
-        margin: 0;
-        padding: 0;
-        width: 100%;
-        height: 100%;
-    }
+.full-message {
+    @extend .w-100;
+    @extend .overflow-hidden;
+    height: $panel-message-height !important;
+    border-bottom: solid $border-color 1px;
+    font-size: 90%;
+    display: none;
+}
+
+#everything {
+    @extend .d-flex;
+    @extend .flex-column;
+    @extend .full-content;
+}
+
+#columns {
+    @extend .position-relative;
+    flex: 1;
+}
+
+#background {
+    @extend .full-content;
+    z-index: -1;
+}
+
+// Used for dragging panels, popup menus, to deal with capturing clicks in iframes
+#dd-helper {
+    @extend .full-content;
+    opacity: 0;
+    z-index: 900; // Bootstrap elements start at 1000
+    display: none;
 }
 
 // ==== Panel layout styles ====
 
-// Layout the paneled UI using flexbox.
-
-#everything {
-    display: flex;
-    flex-direction: column;
-    position: absolute;
-    top: 0;
-    left: 0;
-    margin: 0;
-    padding: 0;
-    width: 100%;
-    height: 100%;
-}
-
-#columns {
-    // Fill extra space in parent
-    flex: 1;
-    // Allow columns to be absolutely positioned inside
-    position: relative;
-}
-
-#background {
-    position: absolute;
-    background: #fff;
-    z-index: -1;
-    top: 0;
-    left: 0;
-    margin: 0;
-    padding: 0;
-    width: 100%;
-    height: 100%;
-}
-
-#messagebox {
-    width: 100%;
-    height: $panel-message-height !important;
-    overflow: hidden;
-    border-bottom: solid $border-default-color 1px;
-    font-size: 90%;
-    display: none;
-}
-
-#inactivebox {
-    width: 100%;
-    height: $panel-message-height !important;
-    overflow: hidden;
-    border-bottom: solid $border-default-color 1px;
-    font-size: 90%;
-    display: none;
-}
-
-// Panels
 #left,
 #center,
 #right {
-    position: absolute;
-    top: 0;
-    height: 100%;
-    overflow: hidden;
-    background: white;
+    @extend .position-absolute;
+    @extend .h-100;
+    @extend .overflow-hidden;
 }
 #left {
+    @extend .unified-panel;
     left: 0px;
     width: $panel-width;
     border-right: $layout-border;
 }
 #right {
+    @extend .unified-panel;
     right: 0px;
     width: $panel-width;
     border-left: $layout-border;
 }
+#right > .unified-panel-footer {
+    .drag {
+        left: 0;
+    }
+}
 #center {
+    @extend .overflow-hidden;
     left: $panel-width;
     right: $panel-width;
-    overflow: hidden;
     .center-container {
-        position: absolute;
-        width: 100%;
-        height: 100%;
+        @extend .position-absolute;
+        @extend .w-100;
+        @extend .h-100;
         .center-panel {
+            @extend .position-absolute;
+            @extend .w-100;
+            @extend .h-100;
+            @extend .overflow-auto;
             display: none;
-            position: absolute;
-            width: 100%;
-            height: 100%;
             padding: $margin-h $margin-v;
-            overflow: auto;
-            background: $brand-white;
+            background: $white;
         }
         .center-frame {
-            position: absolute;
-            width: 100%;
-            height: 100%;
+            @extend .position-absolute;
+            @extend .w-100;
+            @extend .h-100;
         }
     }
     // Replaces unnecessary if/then logic in base_panels.mako
@@ -191,34 +183,34 @@ body {
     }
 }
 
-#left,
-#right,
-.unified-panel {
-    background: $panel-bg-color;
-    display: flex;
-    flex-direction: column;
-}
+// ==== Unified panel styles ====
 
+.unified-panel {
+    display: flex;
+    @extend .flex-column;
+    background: $panel-bg-color;
+}
 .unified-panel-header {
     @extend .unselectable;
-    @extend .mx-3;
+    @extend .px-3;
+    @extend .d-flex;
     height: $panel_header_height;
     font-size: 1rem;
     font-weight: bold;
-    display: flex;
     align-items: center;
     color: $panel-header-text-color;
+    background: $panel-bg-header-color;
     a {
         color: $panel-header-text-color;
     }
     .unified-panel-header-inner {
-        width: 100%;
+        @extend .w-100;
         align-items: center;
         justify-content: space-between;
     }
     .panel-header-buttons {
+        @extend .float-right;
         order: 9999;
-        float: right;
         .panel-header-button {
             text-align: center;
             &:not(:last-child) {
@@ -230,11 +222,19 @@ body {
         }
     }
 }
-
 .unified-panel-controls {
     @extend .px-3;
 }
-
+.unified-panel-body {
+    @extend .p-0;
+    @extend .w-100;
+    @extend .h-100;
+    @extend .overflow-auto;
+    flex: 1;
+}
+.unified-panel-body-background {
+    background: none repeat scroll 0 0 $panel-bg-color;
+}
 .unified-panel-footer {
     @extend .unselectable;
     position: relative;
@@ -262,15 +262,9 @@ body {
     }
 }
 
-#right > .unified-panel-footer {
-    .drag {
-        left: 0;
-    }
-}
-
 // Needs to be outside panel to show when hidden
 .panel-collapse {
-    @extend .fa-icon;
+    @extend .fa;
     $border-color: darken($panel-footer-bg-color, 20%);
     font-size: 4/3em;
     cursor: pointer;
@@ -315,35 +309,6 @@ body {
     }
 }
 
-.menu-bg {
-    background: whiteSmoke top repeat-x;
-}
-
-div.unified-panel-body {
-    width: 100%;
-    height: 100%;
-    padding: 0px;
-    flex: 1;
-    overflow: auto;
-}
-
-div.unified-panel-body-background {
-    background: none repeat scroll 0 0 $panel-bg-color;
-}
-
-// Used for dragging panels, popup menus, to deal with capturing clicks in iframes
-#dd-helper {
-    background: white;
-    opacity: 0;
-    z-index: 900; // Bootstrap elements start at 1000
-    position: absolute;
-    top: 0;
-    left: 0;
-    width: 100%;
-    height: 100%;
-    display: none;
-}
-
 // Messages for message box, slightly different style
 
 .panel-error-message,
@@ -379,10 +344,11 @@ div.unified-panel-body-background {
     }
 }
 
-// Masthead
+// ==== Masthead ====
+
 #masthead {
-    padding: 0;
-    margin-bottom: 0px;
+    @extend .p-0;
+    @extend .mb-0;
     background-color: $brand-dark;
     height: $masthead-height;
     .navbar-nav {
@@ -395,48 +361,47 @@ div.unified-panel-body-background {
             align-items: center;
             &.active {
                 background: darken($brand-dark, 10%);
+                .nav-link {
+                    color: $white;
+                }
             }
             .nav-link {
                 cursor: pointer;
                 text-decoration: none;
+                color: $gray-300;
                 &:hover {
-                    color: $dropdown-link-active-color;
+                    color: $brand-toggle;
                 }
                 &.nav-icon {
                     font-size: 1.7em;
                 }
                 &.toggle {
-                    color: $dropdown-link-active-color;
+                    color: $brand-toggle;
                 }
             }
             .nav-note {
-                font-weight: bold;
-                font-size: 10px;
-                position: relative;
-                right: 5px;
-                top: 10px;
-                color: $dropdown-link-active-color;
-                width: 0px;
+                @extend .font-weight-bold;
+                @extend .position-relative;
+                right: 0.4rem;
+                top: 0.7rem;
+                font-size: 0.7rem;
+                color: $brand-toggle;
+                width: 0;
             }
         }
     }
     .navbar-brand {
-        position: absolute;
-        left: 0;
-        // top: 0;
+        @extend .position-absolute;
+        @extend .font-weight-bold;
+        left: 0.3rem;
+        top: 0;
         font-family: verdana;
-        font-weight: bold;
-        font-size: 20px;
-        // line-height: 1;
-        color: $white;
-        // Override margin and padding due to shorter navbar height
-        padding: 5px 20px 12px;
-        margin-left: -15px;
+        font-size: 1.25rem;
+        color: $gray-300;
         text-decoration: none;
         .navbar-brand-image {
             display: inline;
             width: 26px;
-            // vertical-align: top;
             margin-left: 0.35em;
             border: none;
         }
@@ -446,9 +411,10 @@ div.unified-panel-body-background {
     }
 }
 
+// ==== Quota meter styles ====
+
 .quota-meter-container {
     position: absolute;
-    // top: 0;
     right: 0;
     height: 32px;
 }
@@ -528,11 +494,11 @@ div.metadataFormBody div.metadataFormTitle {
 
 div.metadataFormDisabled div.metadataFormTitle {
     background: #eee;
-    border-color: $border-default-color;
+    border-color: $border-color;
 }
 
 div.metadataFormDisabled {
-    border-color: $border-default-color;
+    border-color: $border-color;
 }
 
 div.metadataHelpBody {
@@ -552,11 +518,11 @@ div.toolFormBody div.toolFormTitle {
 
 div.toolFormDisabled div.toolFormTitle {
     background: #f5f5f5;
-    border-color: $border-default-color;
+    border-color: $border-color;
 }
 
 div.toolFormDisabled {
-    border-color: $border-default-color;
+    border-color: $border-color;
 }
 
 div.toolHelp {
@@ -693,19 +659,6 @@ div.form-row-input label {
     margin-bottom: 10px;
 }
 
-// Selects
-select {
-    padding: 2px;
-    font-size: $font-size-base;
-    line-height: $line-height-base;
-}
-
-select,
-input,
-textarea {
-    font: inherit;
-}
-
 .form-row {
     select,
     textarea,
@@ -718,23 +671,6 @@ textarea {
     display: block;
 }
 
-textarea,
-input[type="text"],
-input[type="password"] {
-    font-size: $font-size-base;
-    line-height: $line-height-base;
-}
-
-// Always style buttons and submits as bootstrap buttons
-input[type="submit"],
-button {
-    @extend .btn;
-    @extend .btn-secondary;
-    &.btn-primary {
-        @extend .btn-primary;
-    }
-}
-
 // Messages
 
 .errormessagelarge,
@@ -792,8 +728,6 @@ button {
     padding: 5px;
     padding-left: 25px;
     min-height: 15px;
-    //border: 1px solid $error_message_border;
-    //background-color: $error_message_bg;
     background-image: url(../../images/error_small.png);
     background-repeat: no-repeat;
     background-position: 5px 6px;
@@ -923,55 +857,49 @@ div.debug {
 }
 
 // Data grid style
-
 .grid-table {
-    width: 100%;
+    @extend .w-100;
 }
 .grid-header {
-    padding-bottom: 1em;
-}
-.grid-header h2 {
-    margin: 0;
-    margin-bottom: 0.5em;
+    @extend .mb-2;
 }
 .grid-header .title {
-    font-weight: bold;
+    @extend .font-weight-bold;
 }
 .grid {
-    padding-top: 1em;
+    @extend .pt-2;
+    @extend .w-100;
     border-collapse: collapse;
-    width: 100%;
 }
 .grid tbody td {
-    line-height: $line-height-base;
-    border-top: solid #dddddd 1px;
-    border-bottom: solid #dddddd 1px;
-    padding: 5px;
+    @extend .border-top;
+    @extend .border-bottom;
+    @extend .p-1;
 }
 .grid tbody td:empty {
-    padding: 0;
+    @extend .p-0;
 }
 .grid thead tr {
     height: 2em;
 }
 .grid thead th {
+    @extend .p-1;
+    @extend .border-top;
+    @extend .border-bottom;
     line-height: $line-height-base;
-    background: $table-heading-bg;
-    color: contrast($table-heading-bg);
-    border-top: solid $table-border-color 1px;
-    border-bottom: solid $table-border-color 1px;
-    padding: 5px;
+    background: $brand-light;
+    color: $text-color;
     text-align: left;
     white-space: nowrap;
 }
 .grid tfoot td {
-    background-color: #f8f8f8;
-    border-top: solid #dddddd 1px;
-    border-bottom: solid #dddddd 1px;
-    padding: 5px;
+    @extend .border-top;
+    @extend .border-bottom;
+    @extend .p-1;
+    background-color: $brand-light;
 }
 .grid .current {
-    background-color: #eeeeff;
+    background-color: lighten($brand-success, 20%);
 }
 
 // Pulled out of grid base
@@ -1077,32 +1005,25 @@ ul.manage-table-actions li {
 }
 
 .state-progress {
-    border: 1px solid gray;
-    position: relative;
-
-    margin-top: 2px;
-    margin-bottom: 1px;
-
+    @extend .position-relative;
+    @extend .m-1;
+    border: $border-default;
     .info {
-        color: $black;
-        background: $white;
+        color: $text-color;
+        background: $body-bg;
     }
-
     .new {
         background: $state-default-bg;
     }
-
     .running {
         background: $state-running-bg;
     }
-
     .ok {
         background: $state-success-bg;
     }
-
     .note {
-        margin-left: 1em;
-        position: absolute;
+        @extend .position-absolute;
+        @extend .ml-2;
     }
 }
 
@@ -1170,6 +1091,7 @@ a.btn {
 }
 a.action-button {
     color: $btn-default-color;
+    background: $btn-default-bg;
     text-decoration: none;
 }
 .action-button > img {
@@ -1370,7 +1292,7 @@ div.permissionContainer {
 
 .editable-text:hover {
     cursor: text;
-    border: dotted $border-default-color 1px;
+    border: dotted $border-color 1px;
 }
 
 .icon-button.multiinput {
@@ -1445,11 +1367,13 @@ div.toolPanelLabel {
     @extend .px-3;
     font-weight: bold;
     font-size: $h4-font-size;
-    color: $gray-600;
+    color: $text-muted;
     text-transform: uppercase;
 }
 
-div.toolSectionTitle, div.toolTitle, div.toolTitleNoSection {
+div.toolSectionTitle,
+div.toolTitle,
+div.toolTitleNoSection {
     display: block;
     .labels {
         float: right;
@@ -1753,7 +1677,7 @@ div.toolSectionWrapper {
     @extend .fa;
     @extend .fa-circle;
     @extend .mt-1;
-    color: $white;
+    color: $brand-light;
     position: absolute;
     z-index: 1500;
     > icon {
@@ -1791,7 +1715,7 @@ div.toolSectionWrapper {
 }
 .mark-terminal {
     cursor: pointer;
-    color: darken($border-default-color, 20%);
+    color: $text-muted;
     &.mark-terminal-active {
         color: $brand-success;
     }
diff --git a/client/galaxy/style/scss/charts.scss b/client/galaxy/style/scss/charts.scss
index 93b42b8c966..49bd3e765c2 100644
--- a/client/galaxy/style/scss/charts.scss
+++ b/client/galaxy/style/scss/charts.scss
@@ -1,4 +1,5 @@
 .charts-client {
+    background: $body-bg;
     .charts-buttons {
         @extend .float-right;
         position: absolute;
@@ -7,7 +8,7 @@
         width: 170px;
         top: 4px;
         .btn {
-            background: white;
+            background: $body-bg;
             color: $panel-header-text-color;
             border: none;
             .icon {
@@ -60,8 +61,8 @@
         float: left;
         width: 30%;
         height: 100vh;
-        padding-bottom: 32px;
-        padding-top: 32px;
+        padding-bottom: 40px;
+        padding-top: 40px;
         overflow: hidden;
         display: flex;
         flex-direction: column;
diff --git a/client/galaxy/style/scss/dataset.scss b/client/galaxy/style/scss/dataset.scss
index 28a28b04dfa..9d897df2859 100644
--- a/client/galaxy/style/scss/dataset.scss
+++ b/client/galaxy/style/scss/dataset.scss
@@ -4,7 +4,7 @@
 // ---------------------------------------------------------------------------- dataset states
 //.dataset .state-icon {
 .state-icon {
-    @extend .fa-icon;
+    @extend .fa;
     display: inline-block;
     margin-right: 4px;
     vertical-align: middle;
@@ -309,17 +309,15 @@
             @extend %vertical-spacing;
             .annotation {
                 @extend %info-section;
-                //white-space: pre-line;
                 white-space: pre-wrap;
                 overflow: auto;
             }
             // fake placeholder for editable text annotation
             .annotation:empty:after {
-                position: relative;
-                top: -4px;
-                font-size: 10px;
-                font-style: italic;
-                color: grey;
+                @extend .position-relative;
+                @extend .font-italic;
+                @extend .h6;
+                color: $text-muted;
                 //TODO: move out for localization
                 content: "Click here to edit annotation";
             }
diff --git a/client/galaxy/style/scss/frame.scss b/client/galaxy/style/scss/frame.scss
index ef956308d4a..20ed7a56b47 100644
--- a/client/galaxy/style/scss/frame.scss
+++ b/client/galaxy/style/scss/frame.scss
@@ -1,5 +1,5 @@
 $frame-zindex: 1000;
-$frame-default-border: $border-default-color;
+$frame-default-border: $border-color;
 
 .galaxy-frame {
     .corner {
@@ -19,7 +19,7 @@ $frame-default-border: $border-default-color;
         height: 100%;
         width: 100%;
         opacity: 0.5;
-        background: $brand-dark;
+        background: $brand-light;
         overflow: auto;
     }
 
diff --git a/client/galaxy/style/scss/history.scss b/client/galaxy/style/scss/history.scss
index 4e4686de8d8..4beb1143daa 100644
--- a/client/galaxy/style/scss/history.scss
+++ b/client/galaxy/style/scss/history.scss
@@ -39,13 +39,13 @@
         .annotation-display {
             display: none;
             margin-bottom: 8px;
+            color: $text-muted;
             .prompt {
                 display: block;
                 margin: 0px;
                 padding: 0px;
                 font-size: 90%;
                 font-weight: normal;
-                color: #555;
             }
             .prompt:after {
                 content: ":";
@@ -66,7 +66,7 @@
                 top: -4px;
                 font-size: 10px;
                 font-style: italic;
-                color: grey;
+                color: $text-muted;
                 //TODO: move out for localization
                 content: "Click here to edit annotation";
             }
@@ -77,13 +77,11 @@
                 width: 100%;
             }
         }
-
         .list-pagination {
             width: 100%;
             text-align: center;
             margin: 0;
             border-top: 1px solid $btn-default-border;
-
             button {
                 margin: 0;
                 padding: 0;
@@ -98,7 +96,6 @@
                 -moz-appearance: none;
                 -webkit-appearance: none;
                 appearance: none;
-
                 margin: 0;
                 padding: 0;
                 width: 48%;
@@ -107,7 +104,6 @@
                 box-shadow: none;
                 text-align: center;
                 text-align-last: center;
-
                 &:focus {
                     outline: none;
                 }
@@ -123,7 +119,7 @@
                 border-radius: 0px;
                 background: transparent;
                 &.pages {
-                    color: grey;
+                    color: $text-muted;
                     text-decoration: underline;
                 }
                 &:hover,
@@ -135,7 +131,6 @@
                     text-decoration: none;
                 }
             }
-
             &:hover > *:not([disabled]) {
                 color: $btn-default-color;
             }
@@ -145,7 +140,7 @@
     // the help text that appears above the drop target
     .history-drop-target-help {
         margin: 10px 10px 4px 10px;
-        color: grey;
+        color: $text-muted;
         font-size: 80%;
         font-style: italic;
         text-align: center;
@@ -163,7 +158,7 @@
         overflow-y: auto;
 
         &:not(:empty) {
-            border-top: 1px solid $border-default-color;
+            border-top: 1px solid $border-color;
         }
         &:empty {
             flex-grow: 0 !important;
@@ -183,7 +178,7 @@
         width: 100%;
         padding: 16px;
         text-align: center;
-        color: grey;
+        color: $text-color;
     }
 
     .history-content.dataset,
@@ -363,7 +358,7 @@
     $mph-column_width: 312px;
     $mph-border_width: 1px;
     $mph-column_gap: 8px;
-    $mph-header_height: 29px;
+    $mph-header_height: 40px;
     $mph-footer_height: 0;
     $mph-controls_height: 20px;
 
@@ -427,14 +422,15 @@
     & > .header,
     & > .footer {
         width: 100%;
-        background-color: lightgrey;
-        .btn {
-            height: 21px;
-        }
+        background-color: $white;
     }
     & > .header {
         min-height: $mph-header_height;
         max-height: $mph-header_height;
+        .search-control {
+            width: 300px;
+            float: left;
+        }
         // popover containing sorting and filters
         .more-options {
             .btn {
@@ -466,7 +462,6 @@
     // the header/footers controls
     .control-column {
         margin-top: 4px;
-
         .btn {
             @extend .btn-sm;
         }
@@ -477,9 +472,8 @@
         .header-info {
             display: inline-block;
             padding: 2px 4px 2px 4px;
-            color: grey;
+            color: $text-muted;
         }
-
         &.control-column-right,
         &.control-column-left {
             margin-right: 8px;
@@ -512,7 +506,7 @@
     .middle {
         min-width: 100%;
         margin: 0px 0px 0px 0px;
-        background-color: white;
+        background-color: $white;
         padding: $mph-column_gap 0px;
     }
 
@@ -524,7 +518,7 @@
         &:first-child {
             position: fixed;
             z-index: 10;
-            background-color: white;
+            background-color: $white;
             width: $mph-column_width + $mph-column_gap;
             padding-left: $mph-column_gap;
 
@@ -544,7 +538,7 @@
         .panel-controls {
             width: 100%;
             height: ($mph-controls_height + 4);
-            background-color: white;
+            background-color: $white;
 
             .btn {
                 @extend .btn-sm;
@@ -557,20 +551,17 @@
             }
             .current-label {
                 display: inline-block;
-                color: grey;
+                color: $text-muted;
                 padding-left: 2px;
                 margin-top: 2px;
             }
         }
         .history-panel {
             width: 100%;
-
             border: $mph-border_width solid grey;
             border-radius: 3px 3px 0px 0px;
             background-color: $panel-bg-color;
-
             overflow: auto;
-
             & > .controls .subtitle {
                 min-height: 15px;
                 margin: -4px 0px 8px;
@@ -578,7 +569,6 @@
                     content: ", ";
                 }
             }
-
             & > .controls .list-pagination {
                 // text a bit smaller for all
                 font-size: 90%;
@@ -597,7 +587,7 @@
         transform-origin: left top 0;
         margin-left: 16px;
         white-space: nowrap;
-        color: grey;
+        color: $text-muted;
         span {
             // space btwn icon and text
             margin-right: 8px;
diff --git a/client/galaxy/style/scss/job.scss b/client/galaxy/style/scss/job.scss
index a855e1c6274..789f3a6507e 100644
--- a/client/galaxy/style/scss/job.scss
+++ b/client/galaxy/style/scss/job.scss
@@ -1,6 +1,6 @@
 // ---------------------------------------------------------------------------- generic panel list items
 .job.list-item {
-    border: 1px solid $border-default-color;
+    border: 1px solid $border-color;
 
     .title-bar {
         .subtitle {
@@ -45,7 +45,7 @@
                 .list-item {
                     border: 0px;
                     border-radius: 0px;
-                    border-top: 1px solid $border-default-color;
+                    border-top: 1px solid $border-color;
                     &:last-child {
                     }
                 }
diff --git a/client/galaxy/style/scss/library.scss b/client/galaxy/style/scss/library.scss
index ca7b392c029..503c3e1a969 100644
--- a/client/galaxy/style/scss/library.scss
+++ b/client/galaxy/style/scss/library.scss
@@ -83,7 +83,7 @@
         color: $brand-light;
     }
     tr.table-primary td a {
-        color: $brand-white;
+        color: $white;
     }
     a.dark {
         color: white;
diff --git a/client/galaxy/style/scss/list-item.scss b/client/galaxy/style/scss/list-item.scss
index d5fe3b18b02..65a89c763d4 100644
--- a/client/galaxy/style/scss/list-item.scss
+++ b/client/galaxy/style/scss/list-item.scss
@@ -13,11 +13,11 @@ $vertical-gap: 8px;
 
 %help-text {
     font-weight: normal;
-    color: #555;
+    color: $gray-700;
 }
 
 .list-item {
-    border: 1px solid $border-default-color;
+    border: 1px solid $border-color;
 
     .vertical-spacing {
         @extend %vertical-spacing;
@@ -51,7 +51,7 @@ $vertical-gap: 8px;
     .help-text {
         @extend %help-text;
         font-weight: normal;
-        color: #555;
+        color: $gray-700;
     }
 
     .selector {
@@ -88,14 +88,14 @@ $vertical-gap: 8px;
             text-decoration: underline;
         }
         .subtitle {
-            color: #777;
+            color: $text-muted;
             font-size: 90%;
             a {
                 color: inherit;
             }
         }
         .state-description {
-            color: #777;
+            color: $text-muted;
             font-size: 90%;
             a {
                 color: inherit;
@@ -156,7 +156,7 @@ $vertical-gap: 8px;
             }
         }
         .subtitle {
-            color: #777;
+            color: $text-muted;
             font-size: 90%;
             a {
                 color: inherit;
@@ -225,7 +225,7 @@ $vertical-gap: 8px;
     background: white;
     padding: 4px;
     .list-items {
-        border: 1px solid $border-default-color;
+        border: 1px solid $border-color;
         border-radius: 3px;
         .list-item {
             &:first-child {
diff --git a/client/galaxy/style/scss/overrides.scss b/client/galaxy/style/scss/overrides.scss
index 481e1143590..5c39659a089 100644
--- a/client/galaxy/style/scss/overrides.scss
+++ b/client/galaxy/style/scss/overrides.scss
@@ -25,7 +25,7 @@ pre {
 }
 
 .btn-secondary {
-    border: 1px solid $border-default-color;
+    border: $border-default;
 }
 
 .popover .popover-body {
@@ -38,6 +38,13 @@ pre {
     }
 }
 
+.dropdown-item,
+.dropdown-header {
+    color: $text-color;
+}
+
+// Input fields
+
 input[type="checkbox"],
 input[type="radio"] {
     margin-left: 0.5ex;
@@ -45,6 +52,35 @@ input[type="radio"] {
     float: left;
 }
 
+select {
+    padding: 2px;
+    font-size: $font-size-base;
+    line-height: $line-height-base;
+}
+
+select,
+input,
+textarea {
+    font: inherit;
+}
+
+textarea,
+input[type="text"],
+input[type="password"] {
+    font-size: $font-size-base;
+    line-height: $line-height-base;
+}
+
+// Always style buttons and submits as bootstrap buttons
+input[type="submit"],
+button {
+    @extend .btn;
+    @extend .btn-secondary;
+    &.btn-primary {
+        @extend .btn-primary;
+    }
+}
+
 // Modal -- wider by default, scroll like Trello
 
 .modal-dialog {
@@ -64,6 +100,14 @@ input[type="radio"] {
     @extend .mb-2;
 }
 
+.tabbable {
+    .nav-tabs {
+        .nav-item {
+            cursor: pointer;
+        }
+    }
+}
+
 // Don't make blockquotes very large since they're often used in the toolform
 // and this does not look nice to have a quoted portion of a tool's help
 // documentation be rendered 150% larger.
@@ -86,7 +130,10 @@ pre.code {
 }
 
 // increase visibility of links within alert boxes
-.alert-info, .alert-danger, .alert-warning, .alert-success {
+.alert-info,
+.alert-danger,
+.alert-warning,
+.alert-success {
     a {
         font-weight: bold;
     }
@@ -96,6 +143,6 @@ pre.code {
 .dropdown-header {
     font-size: 1rem;
     color: $brand-dark;
-    padding: .5rem 1.5rem .5rem 1rem;
+    padding: 0.5rem 1.5rem 0.5rem 1rem;
     font-weight: bold;
 }
diff --git a/client/galaxy/style/scss/theme/blue.scss b/client/galaxy/style/scss/theme/blue.scss
index a6d2e196b6d..68dfaa5b055 100644
--- a/client/galaxy/style/scss/theme/blue.scss
+++ b/client/galaxy/style/scss/theme/blue.scss
@@ -7,20 +7,26 @@ $brand-warning: #fe7f02;
 $brand-danger: #e31a1e;
 $brand-light: #f8f9fa;
 $brand-dark: #2c3143;
-$brand-white: #fff;
 $brand-toggle: gold;
 
-// Grays from Bootstrap 4 _variables.scss
-$white: $brand-white;
+// Text colors
+$text-color: $brand-dark;
+$text-muted: lighten($text-color, 10%);
+$border-color: lighten($text-color, 60%);
+
+// Light grays for backgrounds
+$white: lighten($brand-light, 15%); // body background
 $gray-100: $brand-light;
-$gray-200: darken($gray-100, 5%); // welcome background
-$gray-300: darken($gray-100, 10%);
-$gray-400: darken($gray-100, 20%); // input borders
-$gray-500: darken($gray-100, 40%);
-$gray-600: darken($gray-100, 60%); // text-muted
-$gray-700: darken($gray-100, 70%);
-$gray-800: darken($gray-100, 80%);
-$gray-900: darken($gray-100, 90%); // text-regular
+$gray-200: darken($brand-light, 5%); // welcome background
+$gray-300: darken($brand-light, 10%);
+
+// Dark grays for foregrounds
+$gray-900: $text-color;
+$gray-800: $text-muted;
+$gray-700: $text-muted;
+$gray-600: $text-muted;
+$gray-500: $text-muted;
+$gray-400: $border-color;
 $black: $brand-dark;
 
 // These variables don't actually determine the colors in Bootstrap 4, instead
@@ -84,19 +90,22 @@ $h6-font-size: $font-size-base * 0.85; // default 1
 // Increase contrast of dropdown items
 $dropdown-link-hover-color: $brand-light;
 $dropdown-link-hover-bg: $brand-primary;
-$dropdown-link-active-color: $brand-toggle;
+
+// Color of input elements
+$input-color: $text-color;
+$input-color-placeholder: $text-muted;
 
 // Galaxy Variables (not used by bootstrap)
 $body-bg: $white;
-$text-color: $gray-900;
 
 // Masthead
 $masthead-height: 3rem;
 
 // Side panels
-$panel-bg-color: $gray-100;
+$panel-bg-color: $brand-light;
 $panel-text-color: $text-color;
 $panel-header-text-color: $text-color;
+$panel-bg-header-color: $panel-bg-color;
 $panel-footer-bg-color: $panel-bg-color;
 $panel-message-height: 2.5rem;
 $panel-width: 18rem;
@@ -115,13 +124,12 @@ $layout-border: none;
 $border-radius-base: 0.1875rem;
 $border-radius-large: 0.3125rem;
 $border-radius-extralarge: 1rem;
-$border-default-color: $gray-400;
-$border-default: 1px solid $border-default-color;
+$border-default: 1px solid $border-color;
 
 // Buttons
 $btn-default-color: $text-color;
 $btn-default-bg: $gray-200;
-$btn-default-border: $border-default-color;
+$btn-default-border: $border-color;
 
 // Forms
 $form-heading-bg: $panel-bg-color;
@@ -130,17 +138,17 @@ $form-border: darken($form-heading-bg, 20%);
 // Table
 $table-heading-bg: $panel-bg-color;
 $table-bg-accent: darken($panel-bg-color, 5%);
-$table-border-color: darken($table-heading-bg, 20%);
+$table-border-color: $border-color;
 
 // Additional state colors
 $state-default-bg: $gray-200;
-$state-default-border: $border-default-color;
+$state-default-border: $border-color;
 $state-paused-bg: lighten($brand-info, 50%);
 $state-running-bg: lighten($brand-warning, 40%);
-$state-running-border: $border-default-color;
+$state-running-border: $border-color;
 
 // Workflow editor
-$workflow-editor-bg: $brand-white;
+$workflow-editor-bg: $white;
 $workflow-overview-bg: $gray-200;
 
 // Margins
diff --git a/client/galaxy/style/scss/ui.scss b/client/galaxy/style/scss/ui.scss
index 8688b25bd28..7de7815ab57 100644
--- a/client/galaxy/style/scss/ui.scss
+++ b/client/galaxy/style/scss/ui.scss
@@ -46,6 +46,7 @@ $ui-margin-horizontal-large: $margin-v * 2;
     .modal-backdrop {
         z-index: -1;
         opacity: 0.5;
+        background: $brand-light;
     }
     .modal-body {
         position: static;
@@ -84,13 +85,6 @@ $ui-margin-horizontal-large: $margin-v * 2;
     cursor: pointer;
 }
 
-// tabs
-.tabbable {
-    .nav-item {
-        cursor: pointer;
-    }
-}
-
 // thumbnails
 .ui-thumbnails {
     .ui-thumbnails-item {
@@ -105,7 +99,7 @@ $ui-margin-horizontal-large: $margin-v * 2;
             height: 86px;
             font-size: 4em;
             padding: 20px 26px;
-            color: lighten($brand-primary, 10%);
+            color: $text-color;
         }
         .ui-thumbnails-text {
             word-wrap: break-word;
@@ -253,9 +247,9 @@ $ui-margin-horizontal-large: $margin-v * 2;
 
 // popovers
 .popover {
-    max-width: 700px;
+    max-width: 70%;
     .popover-header {
-        color: $brand-white;
+        color: $brand-light;
         background-color: $brand-primary;
         i {
             @extend .float-right;
@@ -422,9 +416,6 @@ $ui-margin-horizontal-large: $margin-v * 2;
             -webkit-appearance: none;
             -moz-border-radius: $border-radius-base;
             line-height: 1.5rem;
-            .select2-chosen {
-                white-space: normal;
-            }
             .select2-arrow {
                 display: none;
             }
@@ -477,12 +468,3 @@ $ui-margin-horizontal-large: $margin-v * 2;
     border: 2px solid $state-success-bg;
     background: lighten($state-success-bg, 10%) !important;
 }
-
-// select2 adjustments
-.select2-drop-active,
-.select2-drop-above.select2-drop-active {
-    border: 1px solid $border-default-color;
-    .select2-search {
-        @extend .pt-1;
-    }
-}
diff --git a/client/galaxy/style/scss/ui/icon-btn.scss b/client/galaxy/style/scss/ui/icon-btn.scss
index 106f681df42..0bafffa2bd0 100644
--- a/client/galaxy/style/scss/ui/icon-btn.scss
+++ b/client/galaxy/style/scss/ui/icon-btn.scss
@@ -1,7 +1,6 @@
 $icon-btn-size: 22px;
 $icon-btn-margin: 2px;
 $icon-btn-color: $btn-default-color;
-
 $icon-btn-bg: $btn-default-bg;
 $icon-btn-border: $btn-default-border;
 
diff --git a/client/galaxy/style/scss/ui/paired-collection-creator.scss b/client/galaxy/style/scss/ui/paired-collection-creator.scss
index 27de57e1771..d17cb4cb296 100644
--- a/client/galaxy/style/scss/ui/paired-collection-creator.scss
+++ b/client/galaxy/style/scss/ui/paired-collection-creator.scss
@@ -153,8 +153,6 @@
             margin-bottom: 17px;
             overflow: hidden;
             padding: 15px;
-            background: #f8f8f8;
-
             &:not(.expanded) {
                 // chosen to match alert - dependent on line height and .alert padding
                 max-height: 49px;
diff --git a/client/galaxy/style/scss/ui/search-input.scss b/client/galaxy/style/scss/ui/search-input.scss
index 1b35779a931..a41aad6e741 100644
--- a/client/galaxy/style/scss/ui/search-input.scss
+++ b/client/galaxy/style/scss/ui/search-input.scss
@@ -1,5 +1,8 @@
 .search-input {
     @extend .mb-2;
+    ::placeholder {
+        color: $text-muted;
+    }
     .search-clear,
     .search-loading {
         @extend .mr-2;
@@ -8,7 +11,7 @@
         float: right;
         margin-top: -25px;
         font-size: 1.4em;
-        color: $gray-500;
+        color: $text-muted;
     }
     .search-clear:hover {
         color: $brand-info;
@@ -28,7 +31,7 @@
         border: $border-default;
         @include border-radius($border-radius-extralarge);
         max-width: auto;
-        background: $brand-white;
+        background: $white;
     }
     .search-query:focus {
         border-color: $brand-info;
diff --git a/client/galaxy/style/scss/upload.scss b/client/galaxy/style/scss/upload.scss
index 01712bbcf37..79ffeb983ca 100644
--- a/client/galaxy/style/scss/upload.scss
+++ b/client/galaxy/style/scss/upload.scss
@@ -39,6 +39,7 @@
 
 .upload-input {
     font-size: $font-size-base;
+    color: $text-color;
     height: 20px;
     line-height: 18px;
 }
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 398ca602f96..5e65ae3cb22 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -3505,6 +3505,17 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``workflow_schedulers_config_file``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Optional configuration file similar to `job_config_file` to
+    specify which Galaxy processes should schedule workflows.
+:Default: ``config/workflow_schedulers_conf.xml``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~
 ``cache_user_job_count``
 ~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/doc/source/admin/nginx.md b/doc/source/admin/nginx.md
index f73f98a9f67..33763b63095 100644
--- a/doc/source/admin/nginx.md
+++ b/doc/source/admin/nginx.md
@@ -242,9 +242,9 @@ previous section:
 
 Galaxy sends files (e.g. dataset downloads) by opening the file and streaming it in chunks through the proxy server.
 However, this ties up the Galaxy process, which can impact the performance of other operations (see [Production Server
-Configuration](production.md) for a more in-depth explanation). 
+Configuration](production.md) for a more in-depth explanation).
 
-Nginx can assume this task instead and, as an added benefit, speed up downloads. In addition, both the IGV genome browser and JBrowse tool (run within Galaxy) require support for the HTTP *Range* header, and this is only available if the proxy serves datasets.
+Nginx can assume this task instead and, as an added benefit, speed up downloads. In addition, the Integrative Genomics Viewer (IGV), the Integrated Genome Browser (IGB), and the JBrowse tool (run within Galaxy) require support for the HTTP *Range* header, and this is only available if the proxy serves datasets.
 This is accomplished through the use of the special `X-Accel-Redirect` header. Dataset security is maintained in this configuration because nginx will still check with Galaxy to ensure that the requesting user has permission to access the dataset before sending it.
 
 To enable it, add the following to your Galaxy's `server {}` block:
diff --git a/doc/source/admin/production.md b/doc/source/admin/production.md
index 6234953f783..c7ea2f4b5b2 100644
--- a/doc/source/admin/production.md
+++ b/doc/source/admin/production.md
@@ -49,11 +49,11 @@ Two options are set in the sample `config/galaxy.yml` which should not be enable
 
 During deployment, you may run into problems with failed jobs.  By default, Galaxy removes files related to job execution. You can instruct Galaxy to keep files of failed jobs with: `cleanup_job: onsuccess`
 
-### Switching to a database server
+### Switching to PostgreSQL database server
 
 The most important recommendation is to switch to an actual database server.  By default, Galaxy will use [SQLite](http://www.sqlite.org/), which is a serverless simple file database engine.  Since it's serverless, all of the database processing occurs in the Galaxy process itself.  This has two downsides: it occupies the aforementioned GIL (meaning that the process is not free to do other tasks), and it is not nearly as efficient as a dedicated database server.  There are other drawbacks, too.  When load increases with multiple users, the risk of transactional locks also increases.  Locks will cause (among other things) timeouts and job errors.  If you start with SQLite and then later realize a need for a database server, you'll need to migrate your database or start over.  Galaxy does not provide an internal method to migrate data from SQLite, and although free conversion tools are available on the web, this process is non-trivial.
 
-For this reason, Galaxy also supports [PostgreSQL](https://www.postgresql.org/) and [MySQL](https://dev.mysql.com/). *PostgreSQL is much preferred since we've found it works better with our DB abstraction layer, [SQLAlchemy](https://www.sqlalchemy.org/).*
+For this reason, Galaxy also supports PostgreSQL through our DB abstraction layer, [SQLAlchemy](https://www.sqlalchemy.org/).
 
 To use an external database, you'll need to set one up. That process is outside the scope of this document, but is usually simple. For example, on Debian and Redhat-based Linux distributions, one may already be installed. If not, it should be an `apt-get install` or `yum install` away. On macOS, there are installers available from the [PostgreSQL](https://www.postgresql.org/) website.
 
@@ -61,29 +61,43 @@ Once installed, create a new database user and new database which the new user i
 
 To configure Galaxy, set `database_connection` in Galaxy's config file, `config/galaxy.yml`. The syntax for a database URL is explained in the [SQLAlchemy documentation](https://docs.sqlalchemy.org/en/latest/core/engines.html).
 
-Here follow two example database URLs with username and password:
+An example database URL with username and password:
 
 ```
 postgresql://username:password@localhost/mydatabase
-mysql://username:password@localhost/mydatabase
 ```
 
-
-It's worth noting that some platforms (for example, Debian/Ubuntu) store database sockets in a directory other than the database engine's default. If you're connecting to a database server on the same host as the Galaxy server and the socket is in a non-standard location, you'll need to use these custom arguments (these are the defaults for Debian/Ubuntu, change as necessary for your installation):
+It's worth noting that some platforms (for example, Debian/Ubuntu) store database sockets in a directory other than the database engine's default. If you're connecting to a database server on the same host as the Galaxy server and the socket is in a non-standard location, you'll need to use these custom arguments (this is the default for Debian/Ubuntu, change as necessary for your installation):
 
 ```
 postgresql:///mydatabase?host=/var/run/postgresql
-mysql:///mydatabase?unix_socket=/var/run/mysqld/mysqld.sock
 ```
 
-
 For more hints on available options for the database URL, see the [SQLAlchemy documentation](https://docs.sqlalchemy.org/en/latest/core/engines.html#database-urls).
 
-If you are using [MySQL](https://dev.mysql.com/) and encounter the "MySQL server has gone away" error, please note the `database_engine_option_pool_recycle` option in `config/galaxy.yml`. If this does not solve your problem, see [this post](http://gmod.827538.n3.nabble.com/template/NamlServlet.jtp?macro=print_post&node=2354941) on the Galaxy Development [mailing list](https://galaxyproject.org/mailing-lists/).
+#### Deprecated MySQL support
 
-If you are using [MySQL](https://dev.mysql.com/), please make sure the database output is in UTF-8, otherwise you may encounter Python TypeErrors.
+Postgres database backend is more used and better tested, please use it if you can.
 
-If you are using [MySQL](https://dev.mysql.com/) with [MyISAM](https://dev.mysql.com/doc/refman/8.0/en/myisam-storage-engine.html) table engine, when Galaxy is in multiprocess configuration, workflow steps will [get executed out of order](http://dev.list.galaxyproject.org/Job-execution-order-mixed-up-tt4662488.html) and fail. Use [InnoDB](https://dev.mysql.com/doc/refman/8.0/en/innodb-storage-engine.html) engine instead or switch to [PostgreSQL](https://www.postgresql.org/).
+In the past Galaxy supported [MySQL](https://dev.mysql.com/) but currently there are nontrivial problems associated with it so expect amount of troubleshooting when using it.
+
+Connection string example:
+```
+mysql://username:password@localhost/mydatabase
+```
+
+Connecting using socket on a Debian/Ubuntu system:
+```
+mysql:///mydatabase?unix_socket=/var/run/mysqld/mysqld.sock
+```
+
+Some tips when using MySQL:
+
+* If you encounter the "MySQL server has gone away" error, please note the `database_engine_option_pool_recycle` option in `config/galaxy.yml`. If this does not solve your problem, see [this post](http://gmod.827538.n3.nabble.com/template/NamlServlet.jtp?macro=print_post&node=2354941) on the Galaxy Development [mailing list](https://galaxyproject.org/mailing-lists/).
+
+* Please make sure the database output is in UTF-8, otherwise you may encounter Python TypeErrors.
+
+* If you are using [MySQL](https://dev.mysql.com/) with [MyISAM](https://dev.mysql.com/doc/refman/8.0/en/myisam-storage-engine.html) table engine, when Galaxy is in multiprocess configuration, workflow steps will [get executed out of order](http://dev.list.galaxyproject.org/Job-execution-order-mixed-up-tt4662488.html) and fail. Use [InnoDB](https://dev.mysql.com/doc/refman/8.0/en/innodb-storage-engine.html) engine instead or switch to [PostgreSQL](https://www.postgresql.org/).
 
 ### Using a proxy server
 
diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index f5ba320ff6c..ec139fa8af1 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -156,34 +156,34 @@ class BaseAppConfiguration(object):
         return os.path.join(self.sample_config_dir, path)
 
     def _parse_config_file_options(self, defaults, listify_defaults, config_kwargs):
-        for var, defaults in defaults.items():
+        for var, values in defaults.items():
             if config_kwargs.get(var, None) is not None:
                 path = config_kwargs.get(var)
                 setattr(self, var + '_set', True)
             else:
-                for default in defaults:
-                    if os.path.exists(resolve_path(default, self.root)):
-                        path = default
+                for value in values:
+                    if os.path.exists(resolve_path(value, self.root)):
+                        path = value
                         break
                 else:
-                    path = defaults[-1]
+                    path = values[-1]
                 setattr(self, var + '_set', False)
             setattr(self, var, resolve_path(path, self.root))
 
-        for var, defaults in listify_defaults.items():
+        for var, values in listify_defaults.items():
             paths = []
             if config_kwargs.get(var, None) is not None:
                 paths = listify(config_kwargs.get(var))
             else:
-                for default in defaults:
-                    for path in listify(default):
+                for value in values:
+                    for path in listify(value):
                         if not os.path.exists(resolve_path(path, self.root)):
                             break
                     else:
-                        paths = listify(default)
+                        paths = listify(value)
                         break
                 else:
-                    paths = listify(defaults[-1])
+                    paths = listify(values[-1])
             setattr(self, var, [resolve_path(x, self.root) for x in paths])
 
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index c0485138c37..ff4d675020c 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1701,6 +1701,10 @@ galaxy:
   # tags to do the mapping).
   #workflow_resource_params_mapper: config/workflow_resource_mapper_conf.yml
 
+  # Optional configuration file similar to `job_config_file` to specify
+  # which Galaxy processes should schedule workflows.
+  #workflow_schedulers_config_file: config/workflow_schedulers_conf.xml
+
   # If using job concurrency limits (configured in job_config_file),
   # several extra database queries must be performed to determine the
   # number of jobs a user has dispatched to a given destination.  By
diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index e3c614ecdb0..b255ef91236 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -136,7 +136,7 @@ class ConditionalDependencies(object):
     def check_drmaa(self):
         return ("galaxy.jobs.runners.drmaa:DRMAAJobRunner" in self.job_runners or
                 "galaxy.jobs.runners.slurm:SlurmJobRunner" in self.job_runners or
-                "galaxy.jobs.runners.drmaauniva:DRMAAUnivaJobRunner" in self.job_runners)
+                "galaxy.jobs.runners.univa:UnivaJobRunner" in self.job_runners)
 
     def check_galaxycloudrunner(self):
         return ("galaxycloudrunner.rules" in self.job_rule_modules)
diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
index 6ea38d13cd2..29fa1c06dda 100644
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -231,9 +231,9 @@ class PulsarJobRunner(AsynchronousJobRunner):
         if "job_metrics_config_file" not in conf:
             conf["job_metrics"] = self.app.job_metrics
         if "staging_directory" not in conf:
-            conf["staging_directory"] = "database/pulsar_staging"
+            conf["staging_directory"] = os.path.join(self.app.config.data_dir, "pulsar_staging")
         if "persistence_directory" not in conf:
-            conf["persistence_directory"] = "database/pulsar_persisted_data"
+            conf["persistence_directory"] = os.path.join(self.app.config.data_dir, "pulsar_persisted_data")
         if "galaxy_home" not in conf:
             conf["galaxy_home"] = galaxy_directory()
         self.pulsar_app = pulsar.core.PulsarApp(**conf)
diff --git a/lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh b/lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
index 70491d5b32d..f02d70ce260 100644
--- a/lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
+++ b/lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
@@ -2,7 +2,7 @@ if [ -n "$SLURM_JOB_ID" ]; then
     GALAXY_MEMORY_MB=`scontrol -do show job "$SLURM_JOB_ID" | sed 's/.*\( \|^\)Mem=\([0-9][0-9]*\)\( \|$\).*/\2/p;d'` 2>memory_statement.log
 fi
 if [ -n "$SGE_HGR_h_vmem" ]; then
-    GALAXY_MEMORY_MB_PER_SLOT=`echo "$SGE_HGR_h_vmem" | sed 's/G$/ * 1024/' | bc | cut -d"." -f1` 2>memory_statement.log
+    GALAXY_MEMORY_MB=`echo "$SGE_HGR_h_vmem" | sed 's/G$/ * 1024/' | bc | cut -d"." -f1` 2>memory_statement.log
 fi
 
 if [ -z "$GALAXY_MEMORY_MB_PER_SLOT" -a -n "$GALAXY_MEMORY_MB" ]; then
diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index 54d1442577d..b64a4d28e02 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -1064,7 +1064,7 @@ class ToolTestDescription(object):
         self.exception = processed_test_dict.get("exception", None)
 
         self.output_collections = map(TestCollectionOutputDef.from_dict, processed_test_dict.get("output_collections", []))
-        self.command_line = processed_test_dict.get("command", None)
+        self.command_line = processed_test_dict.get("command_line", None)
         self.stdout = processed_test_dict.get("stdout", None)
         self.stderr = processed_test_dict.get("stderr", None)
         self.expect_exit_code = processed_test_dict.get("expect_exit_code", None)
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 9a07aeed666..cdbc4d6005a 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1245,6 +1245,13 @@ class Tool(Dictifiable):
             self.__ensure_help()
         return self.__help_by_page
 
+    @property
+    def raw_help(self):
+        # may return rst (or Markdown in the future)
+        tool_source = self.__help_source
+        help_text = tool_source.parse_help()
+        return help_text
+
     def __ensure_help(self):
         with HELP_UNINITIALIZED:
             if self.__help is HELP_UNINITIALIZED:
diff --git a/lib/galaxy/tools/cache.py b/lib/galaxy/tools/cache.py
index 70366ed54f3..0132c18d341 100644
--- a/lib/galaxy/tools/cache.py
+++ b/lib/galaxy/tools/cache.py
@@ -1,5 +1,6 @@
 import logging
 import os
+from collections import defaultdict
 from threading import (
     local,
     Lock,
@@ -141,6 +142,7 @@ class ToolShedRepositoryCache(object):
 
     def add_local_repository(self, repository):
         self.cache.repositories.append(repository)
+        self.cache.repos_by_tuple[(repository.tool_shed, repository.owner, repository.name)].append(repository)
 
     @property
     def tool_shed_repositories(self):
@@ -155,8 +157,21 @@ class ToolShedRepositoryCache(object):
             repositories = self.cache.repositories
         return repositories
 
+    @property
+    def tool_shed_repos_by_tuple(self):
+        try:
+            return self.cache.repos_by_tuple
+        except AttributeError:
+            self.rebuild()
+            return self.cache.repos_by_tuple
+
     def rebuild(self):
-        self.cache.repositories = self.app.install_model.context.current.query(self.app.install_model.ToolShedRepository).all()
+        repositories = self.app.install_model.context.current.query(self.app.install_model.ToolShedRepository).all()
+        self.cache.repositories = repositories
+        repos_by_tuple = defaultdict(list)
+        for repository in repositories:
+            repos_by_tuple[(repository.tool_shed, repository.owner, repository.name)].append(repository)
+        self.cache.repos_by_tuple = repos_by_tuple
 
     def get_installed_repository(self, tool_shed=None, name=None, owner=None, installed_changeset_revision=None, changeset_revision=None, repository_id=None):
         try:
@@ -182,12 +197,11 @@ class ToolShedRepositoryCache(object):
                 return repos[0]
             else:
                 return None
-        repos = [repo for repo in self.tool_shed_repositories if repo.tool_shed == tool_shed and repo.owner == owner and repo.name == name]
-        if installed_changeset_revision:
-            repos = [repo for repo in repos if repo.installed_changeset_revision == installed_changeset_revision]
-        if changeset_revision:
-            repos = [repo for repo in repos if repo.changeset_revision == changeset_revision]
-        if repos:
-            return repos[0]
-        else:
-            return None
+        repos = self.tool_shed_repos_by_tuple[(tool_shed, owner, name)]
+        for repo in repos:
+            if installed_changeset_revision and repo.installed_changeset_revision != installed_changeset_revision:
+                continue
+            if changeset_revision and repo.changeset_revision != changeset_revision:
+                continue
+            return repo
+        return None
diff --git a/lib/galaxy/tools/search/__init__.py b/lib/galaxy/tools/search/__init__.py
index 7f68703bc06..2c894bd56cb 100644
--- a/lib/galaxy/tools/search/__init__.py
+++ b/lib/galaxy/tools/search/__init__.py
@@ -6,7 +6,6 @@ import logging
 import re
 import tempfile
 
-from bleach import clean
 from whoosh import analysis
 from whoosh.analysis import StandardAnalyzer
 from whoosh.fields import (
@@ -104,15 +103,15 @@ class ToolBoxSearch(object):
             add_doc_kwds['stub'] = to_unicode(id)
         if tool.labels:
             add_doc_kwds['labels'] = to_unicode(" ".join(tool.labels))
-        if index_help and tool.help:
-            try:
-                raw_html = tool.help.render(host_url="", static_path="")
-                cleantext = clean(raw_html, tags=[''], strip=True).replace('\n', ' ')
-                add_doc_kwds['help'] = to_unicode(cleantext)
-            except Exception:
-                # Don't fail to build index just because a help message
-                # won't render.
-                pass
+        if index_help:
+            raw_help = tool.raw_help
+            if raw_help:
+                try:
+                    add_doc_kwds['help'] = to_unicode(raw_help)
+                except Exception:
+                    # Don't fail to build index just because a help message
+                    # won't render.
+                    pass
         return add_doc_kwds
 
     def search(self, q, tool_name_boost, tool_section_boost, tool_description_boost, tool_label_boost, tool_stub_boost, tool_help_boost, tool_search_limit, tool_enable_ngram_search, tool_ngram_minsize, tool_ngram_maxsize):
diff --git a/lib/galaxy/util/xml_macros.py b/lib/galaxy/util/xml_macros.py
index b02796080e1..7af8c5bd10c 100644
--- a/lib/galaxy/util/xml_macros.py
+++ b/lib/galaxy/util/xml_macros.py
@@ -173,7 +173,7 @@ def _expand_yield_statements(macro_def, expand_el):
             if macro_def_el.tag == "yield":
                 for target in expand_el_children:
                     i += 1
-                    macro_def.insert(i, deepcopy(target))
+                    macro_def.insert(i, target)
                 macro_def.remove(macro_def_el)
                 continue
 
@@ -269,7 +269,7 @@ def _xml_replace(query, targets, parent_map):
     current_index = matching_index
     for target in targets:
         current_index += 1
-        parent_el.insert(current_index, deepcopy(target))
+        parent_el.insert(current_index, target)
     parent_el.remove(query)
 
 
diff --git a/lib/galaxy/visualization/plugins/plugin.py b/lib/galaxy/visualization/plugins/plugin.py
index ee51b2fbd5d..5435f180562 100644
--- a/lib/galaxy/visualization/plugins/plugin.py
+++ b/lib/galaxy/visualization/plugins/plugin.py
@@ -72,8 +72,8 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
         self.config = config
         base_url = context.get('base_url', '')
         self.base_url = '/'.join([base_url, self.name]) if base_url else self.name
-        self.static_path = os.path.join(self.path.replace('./config', './static'), 'static')
-        if os.path.exists(os.path.join(self.static_path, 'logo.png')):
+        self.static_path = self._get_static_path(self.path)
+        if self.static_path and os.path.exists(os.path.join(self.static_path, 'logo.png')):
             self.config['logo'] = '/'.join([self.static_path, 'logo.png'])
         template_cache_dir = context.get('template_cache_dir', None)
         additional_template_paths = context.get('additional_template_paths', [])
@@ -127,6 +127,13 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
             return url_for(controller='visualization', action=self.name)
         return url_for('visualization_plugin', visualization_name=self.name)
 
+    def _get_static_path(self, path):
+        if '/config/' in path:
+            match = path.split('/config/')[-1]
+            return os.path.join('./static', match, 'static')
+        else:
+            log.debug('Visualization has no static path: %s.' % path)
+
     def _get_saved_visualization_config(self, visualization, revision=None, **kwargs):
         """
         Return the config of a saved visualization and revision.
diff --git a/lib/galaxy/visualization/plugins/registry.py b/lib/galaxy/visualization/plugins/registry.py
index 8442484bad2..95983ab7c7f 100644
--- a/lib/galaxy/visualization/plugins/registry.py
+++ b/lib/galaxy/visualization/plugins/registry.py
@@ -189,6 +189,8 @@ class VisualizationsRegistry(object):
         if config is not None:
             plugin = self._build_plugin(plugin_name, plugin_path, config)
             return plugin
+        else:
+            raise ObjectNotFound('Visualization XML not found: %s.' % config_file)
 
     def _build_plugin(self, plugin_name, plugin_path, config):
         # TODO: as builder not factory
diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py
index 569a0c0a3f4..e7d7e2cf7c7 100644
--- a/lib/galaxy/web/framework/webapp.py
+++ b/lib/galaxy/web/framework/webapp.py
@@ -436,14 +436,14 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
             # Decode the cookie value to get the session_key
             try:
                 session_key = self.security.decode_guid(secure_id)
+                if session_key:
+                    # Retrieve the galaxy_session id via the unique session_key
+                    galaxy_session = self.sa_session.query(self.app.model.GalaxySession) \
+                                                    .filter(and_(self.app.model.GalaxySession.table.c.session_key == session_key,
+                                                                 self.app.model.GalaxySession.table.c.is_valid == true())).options(joinedload("user")).first()
             except Exception:
                 # We'll end up creating a new galaxy_session
                 session_key = None
-            if session_key:
-                # Retrieve the galaxy_session id via the unique session_key
-                galaxy_session = self.sa_session.query(self.app.model.GalaxySession) \
-                                                .filter(and_(self.app.model.GalaxySession.table.c.session_key == session_key,
-                                                             self.app.model.GalaxySession.table.c.is_valid == true())).options(joinedload("user")).first()
         # If remote user is in use it can invalidate the session and in some
         # cases won't have a cookie set above, so we need to to check some
         # things now.
diff --git a/lib/galaxy/webapps/galaxy/api/folder_contents.py b/lib/galaxy/webapps/galaxy/api/folder_contents.py
index da81e0229d8..66f66780fbe 100644
--- a/lib/galaxy/webapps/galaxy/api/folder_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py
@@ -98,7 +98,7 @@ class FolderContentsController(BaseAPIController, UsesLibraryMixin, UsesLibraryM
                 #  Access rights are checked on the dataset level, not on the ld or ldda level to maintain consistency
                 dataset = content_item.library_dataset_dataset_association.dataset
                 is_unrestricted = trans.app.security_agent.dataset_is_public(dataset)
-                if trans.user and trans.app.security_agent.dataset_is_private_to_user(trans, dataset):
+                if not is_unrestricted and trans.user and trans.app.security_agent.dataset_is_private_to_user(trans, dataset):
                     is_private = True
                 else:
                     is_private = False
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 74271a6f127..8a7a3df026c 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -552,7 +552,8 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
                     if (trans.security.decode_id(id) in entries):
                         trans.get_user().stored_workflow_menu_entries.remove(entries[trans.security.decode_id(id)])
             # set tags
-            trans.app.tag_handler.set_tags_from_list(user=trans.user, item=stored_workflow, new_tags_list=workflow_dict.get('tags', []))
+            if 'tags' in workflow_dict:
+                trans.app.tag_handler.set_tags_from_list(user=trans.user, item=stored_workflow, new_tags_list=workflow_dict['tags'])
 
             if 'steps' in workflow_dict:
                 try:
@@ -565,9 +566,6 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
                     )
                 except workflows.MissingToolsException:
                     raise exceptions.MessageException("This workflow contains missing tools. It cannot be saved until they have been removed from the workflow or installed.")
-            else:
-                # We only adjusted tags and menu entry
-                return payload
         else:
             message = "Updating workflow requires dictionary containing 'workflow' attribute with new JSON description."
             raise exceptions.RequestParameterInvalidException(message)
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index cee5956577e..ec84757e160 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -2612,6 +2612,14 @@ mapping:
           descriptions (additional types of mappings via these files could be implemented but
           haven't yet - for instance using workflow tags to do the mapping).
 
+      workflow_schedulers_config_file:
+        type: str
+        default: config/workflow_schedulers_conf.xml
+        required: false
+        desc: |
+          Optional configuration file similar to `job_config_file` to specify
+          which Galaxy processes should schedule workflows.
+
       cache_user_job_count:
         type: bool
         default: false
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index f457788bdd5..0f3bf04d632 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1612,7 +1612,8 @@ class AdminToolshed(AdminGalaxy):
                                                               tool_shed=tool_shed_url,
                                                               name=name,
                                                               owner=owner,
-                                                              changeset_revision=changeset_revision)
+                                                              changeset_revision=changeset_revision,
+                                                              refresh=True)
         original_metadata_dict = repository.metadata
         original_repository_dependencies_dict = original_metadata_dict.get('repository_dependencies', {})
         original_repository_dependencies = original_repository_dependencies_dict.get('repository_dependencies', [])
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 433f407800e..38b75969b87 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -594,7 +594,7 @@ class InputModule(WorkflowModule):
         progress.set_outputs_for_input(invocation_step, step_outputs)
 
     def recover_mapping(self, invocation_step, progress):
-        progress.set_outputs_for_input(invocation_step)
+        progress.set_outputs_for_input(invocation_step, already_persisted=True)
 
 
 class InputDataModule(InputModule):
@@ -1305,17 +1305,6 @@ class ToolModule(WorkflowModule):
 
         return complete
 
-    def recover_mapping(self, invocation_step, progress):
-        outputs = {}
-
-        for output_dataset_assoc in invocation_step.output_datasets:
-            outputs[output_dataset_assoc.output_name] = output_dataset_assoc.dataset
-
-        for output_dataset_collection_assoc in invocation_step.output_dataset_collections:
-            outputs[output_dataset_collection_assoc.output_name] = output_dataset_collection_assoc.dataset_collection
-
-        progress.set_step_outputs(invocation_step, outputs)
-
     def _effective_post_job_actions(self, step):
         effective_post_job_actions = step.post_job_actions[:]
         for key, value in self.runtime_post_job_actions.items():
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index 3336139eab3..ae20dcb943f 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -405,7 +405,7 @@ class WorkflowProgress(object):
         else:
             return step_outputs[output_name]
 
-    def set_outputs_for_input(self, invocation_step, outputs=None):
+    def set_outputs_for_input(self, invocation_step, outputs=None, already_persisted=False):
         step = invocation_step.workflow_step
 
         if outputs is None:
@@ -420,7 +420,7 @@ class WorkflowProgress(object):
             elif step_id in self.inputs_by_step_id:
                 outputs['output'] = self.inputs_by_step_id[step_id]
 
-        self.set_step_outputs(invocation_step, outputs)
+        self.set_step_outputs(invocation_step, outputs, already_persisted=already_persisted)
 
     def set_step_outputs(self, invocation_step, outputs, already_persisted=False):
         step = invocation_step.workflow_step
diff --git a/packages/tool_util/tests/test_tool_linters.py b/packages/tool_util/tests/test_tool_linters.py
new file mode 120000
index 00000000000..f72ad5bc7ad
--- /dev/null
+++ b/packages/tool_util/tests/test_tool_linters.py
@@ -0,0 +1 @@
+../../../test/unit/tool_util/test_tool_linters.py
\ No newline at end of file
diff --git a/scripts/cleanup_datasets/cleanup_datasets.py b/scripts/cleanup_datasets/cleanup_datasets.py
index 28f4cb53458..b05cb0e9034 100755
--- a/scripts/cleanup_datasets/cleanup_datasets.py
+++ b/scripts/cleanup_datasets/cleanup_datasets.py
@@ -105,15 +105,15 @@ def main():
     cutoff_time = datetime.utcnow() - timedelta(days=args.days)
     now = strftime("%Y-%m-%d %H:%M:%S")
 
-    print("##########################################")
-    print("\n# %s - Handling stuff older than %i days" % (now, args.days))
+    log.info("##########################################")
+    log.info("\n# %s - Handling stuff older than %i days" % (now, args.days))
 
     if args.info_only:
-        print("# Displaying info only ( --info_only )\n")
+        log.info("# Displaying info only ( --info_only )\n")
     elif args.remove_from_disk:
-        print("Datasets will be removed from disk.\n")
+        log.info("Datasets will be removed from disk.\n")
     else:
-        print("Datasets will NOT be removed from disk.\n")
+        log.info("Datasets will NOT be removed from disk.\n")
 
     if args.delete_userless_histories:
         delete_userless_histories(app, cutoff_time, info_only=args.info_only, force_retry=args.force_retry)
@@ -149,15 +149,15 @@ def delete_userless_histories(app, cutoff_time, info_only=False, force_retry=Fal
                                                app.model.History.table.c.update_time < cutoff_time))
     for history in histories:
         if not info_only:
-            print("Deleting history id ", history.id)
+            log.info("Deleting history id ", history.id)
             history.deleted = True
             app.sa_session.add(history)
             app.sa_session.flush()
         history_count += 1
     stop = time.time()
-    print("Deleted %d histories" % history_count)
-    print("Elapsed time: ", stop - start)
-    print("##########################################")
+    log.info("Deleted %d histories" % history_count)
+    log.info("Elapsed time: ", stop - start)
+    log.info("##########################################")
 
 
 def purge_histories(app, cutoff_time, remove_from_disk, info_only=False, force_retry=False):
@@ -180,7 +180,7 @@ def purge_histories(app, cutoff_time, remove_from_disk, info_only=False, force_r
                                                app.model.History.table.c.update_time < cutoff_time)) \
                                   .options(eagerload('datasets'))
     for history in histories:
-        print("### Processing history id %d (%s)" % (history.id, unicodify(history.name)))
+        log.info("### Processing history id %d (%s)" % (history.id, unicodify(history.name)))
         for dataset_assoc in history.datasets:
             _purge_dataset_instance(dataset_assoc, app, remove_from_disk, info_only=info_only)  # mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable
         if not info_only:
@@ -189,17 +189,17 @@ def purge_histories(app, cutoff_time, remove_from_disk, info_only=False, force_r
             # if we should ever delete info like this from the db though, so commented out for now...
             # for dhp in history.default_permissions:
             #     dhp.delete()
-            print("Purging history id ", history.id)
+            log.info("Purging history id ", history.id)
             history.purged = True
             app.sa_session.add(history)
             app.sa_session.flush()
         else:
-            print("History id %d will be purged (without 'info_only' mode)" % history.id)
+            log.info("History id %d will be purged (without 'info_only' mode)" % history.id)
         history_count += 1
     stop = time.time()
-    print('Purged %d histories.' % history_count)
-    print("Elapsed time: ", stop - start)
-    print("##########################################")
+    log.info('Purged %d histories.' % history_count)
+    log.info("Elapsed time: ", stop - start)
+    log.info("##########################################")
 
 
 def purge_libraries(app, cutoff_time, remove_from_disk, info_only=False, force_retry=False):
@@ -222,15 +222,15 @@ def purge_libraries(app, cutoff_time, remove_from_disk, info_only=False, force_r
     for library in libraries:
         _purge_folder(library.root_folder, app, remove_from_disk, info_only=info_only)
         if not info_only:
-            print("Purging library id ", library.id)
+            log.info("Purging library id ", library.id)
             library.purged = True
             app.sa_session.add(library)
             app.sa_session.flush()
         library_count += 1
     stop = time.time()
-    print('# Purged %d libraries .' % library_count)
-    print("Elapsed time: ", stop - start)
-    print("##########################################")
+    log.info('# Purged %d libraries .' % library_count)
+    log.info("Elapsed time: ", stop - start)
+    log.info("##########################################")
 
 
 def purge_folders(app, cutoff_time, remove_from_disk, info_only=False, force_retry=False):
@@ -254,9 +254,9 @@ def purge_folders(app, cutoff_time, remove_from_disk, info_only=False, force_ret
         _purge_folder(folder, app, remove_from_disk, info_only=info_only)
         folder_count += 1
     stop = time.time()
-    print('# Purged %d folders.' % folder_count)
-    print("Elapsed time: ", stop - start)
-    print("##########################################")
+    log.info('# Purged %d folders.' % folder_count)
+    log.info("Elapsed time: ", stop - start)
+    log.info("##########################################")
 
 
 def delete_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_retry=False):
@@ -301,7 +301,7 @@ def delete_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_r
     library_dataset_ids = [row.id for row in library_dataset_ids_query.execute()]
     dataset_ids = []
     for library_dataset_id in library_dataset_ids:
-        print("######### Processing LibraryDataset id:", library_dataset_id)
+        log.info("######### Processing LibraryDataset id:", library_dataset_id)
         # Get the LibraryDataset and the current LibraryDatasetDatasetAssociation objects
         ld = app.sa_session.query(app.model.LibraryDataset).get(library_dataset_id)
         ldda = ld.library_dataset_dataset_association
@@ -311,16 +311,16 @@ def delete_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_r
         if not ldda.deleted:
             ldda.deleted = True
             app.sa_session.add(ldda)
-            print("Marked associated LibraryDatasetDatasetAssociation id %d as deleted" % ldda.id)
+            log.info("Marked associated LibraryDatasetDatasetAssociation id %d as deleted" % ldda.id)
         for expired_ldda in ld.expired_datasets:
             if not expired_ldda.deleted:
                 expired_ldda.deleted = True
                 app.sa_session.add(expired_ldda)
-                print("Marked associated expired LibraryDatasetDatasetAssociation id %d as deleted" % ldda.id)
+                log.info("Marked associated expired LibraryDatasetDatasetAssociation id %d as deleted" % ldda.id)
         # Mark the LibraryDataset as purged
         ld.purged = True
         app.sa_session.add(ld)
-        print("Marked LibraryDataset id %d as purged" % ld.id)
+        log.info("Marked LibraryDataset id %d as purged" % ld.id)
         app.sa_session.flush()
     # Add all datasets associated with Histories to our list
     dataset_ids.extend([row.id for row in history_dataset_ids_query.execute()])
@@ -330,9 +330,9 @@ def delete_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_r
         if dataset.id in skip:
             continue
         skip.append(dataset.id)
-        print("######### Processing dataset id:", dataset_id)
+        log.info("######### Processing dataset id:", dataset_id)
         if not _dataset_is_deletable(dataset):
-            print("Dataset is not deletable (shared between multiple histories/libraries, at least one is not deleted)")
+            log.info("Dataset is not deletable (shared between multiple histories/libraries, at least one is not deleted)")
             continue
         deleted_dataset_count += 1
         for dataset_instance in dataset.history_associations + dataset.library_associations:
@@ -340,9 +340,9 @@ def delete_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_r
             _purge_dataset_instance(dataset_instance, app, remove_from_disk, info_only=info_only, is_deletable=True)
             deleted_instance_count += 1
     stop = time.time()
-    print("Examined %d datasets, marked %d datasets and %d dataset instances (HDA) as deleted" % (len(skip), deleted_dataset_count, deleted_instance_count))
-    print("Total elapsed time: ", stop - start)
-    print("##########################################")
+    log.info("Examined %d datasets, marked %d datasets and %d dataset instances (HDA) as deleted" % (len(skip), deleted_dataset_count, deleted_instance_count))
+    log.info("Total elapsed time: ", stop - start)
+    log.info("##########################################")
 
 
 def purge_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_retry=False):
@@ -371,18 +371,18 @@ def purge_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_re
         except Exception:
             pass
     stop = time.time()
-    print('Purged %d datasets' % dataset_count)
+    log.info('Purged %d datasets' % dataset_count)
     if remove_from_disk:
-        print('Freed disk space: ', disk_space)
-    print("Elapsed time: ", stop - start)
-    print("##########################################")
+        log.info('Freed disk space: ', disk_space)
+    log.info("Elapsed time: ", stop - start)
+    log.info("##########################################")
 
 
 def _purge_dataset_instance(dataset_instance, app, remove_from_disk, info_only=False, is_deletable=False):
     # A dataset_instance is either a HDA or an LDDA.  Purging a dataset instance marks the instance as deleted,
     # and marks the associated dataset as deleted if it is not associated with another active DatsetInstance.
     if not info_only:
-        print("Marking as deleted: %s id %d (for dataset id %d)" %
+        log.info("Marking as deleted: %s id %d (for dataset id %d)" %
               (dataset_instance.__class__.__name__, dataset_instance.id, dataset_instance.dataset.id))
         dataset_instance.mark_deleted()
         dataset_instance.clear_associated_files()
@@ -390,16 +390,16 @@ def _purge_dataset_instance(dataset_instance, app, remove_from_disk, info_only=F
         app.sa_session.flush()
         app.sa_session.refresh(dataset_instance.dataset)
     else:
-        print("%s id %d (for dataset id %d) will be marked as deleted (without 'info_only' mode)" %
+        log.info("%s id %d (for dataset id %d) will be marked as deleted (without 'info_only' mode)" %
               (dataset_instance.__class__.__name__, dataset_instance.id, dataset_instance.dataset.id))
     if is_deletable or _dataset_is_deletable(dataset_instance.dataset):
         # Calling methods may have already checked _dataset_is_deletable, if so, is_deletable should be True
         _delete_dataset(dataset_instance.dataset, app, remove_from_disk, info_only=info_only, is_deletable=is_deletable)
     else:
         if info_only:
-            print("Not deleting dataset ", dataset_instance.dataset.id, " (will be possibly deleted without 'info_only' mode)")
+            log.info("Not deleting dataset ", dataset_instance.dataset.id, " (will be possibly deleted without 'info_only' mode)")
         else:
-            print("Not deleting dataset %d (shared between multiple histories/libraries, at least one not deleted)" % dataset_instance.dataset.id)
+            log.info("Not deleting dataset %d (shared between multiple histories/libraries, at least one not deleted)" % dataset_instance.dataset.id)
 
 
 def _dataset_is_deletable(dataset):
@@ -411,7 +411,7 @@ def _delete_dataset(dataset, app, remove_from_disk, info_only=False, is_deletabl
     # Marks a base dataset as deleted, hdas/lddas associated with dataset can no longer be undeleted.
     # Metadata files attached to associated dataset Instances is removed now.
     if not is_deletable and not _dataset_is_deletable(dataset):
-        print("This Dataset (%i) is not deletable, associated Metadata Files will not be removed.\n" % (dataset.id))
+        log.info("This Dataset (%i) is not deletable, associated Metadata Files will not be removed.\n" % (dataset.id))
     else:
         # Mark all associated MetadataFiles as deleted and purged and remove them from disk
         metadata_files = []
@@ -429,29 +429,29 @@ def _delete_dataset(dataset, app, remove_from_disk, info_only=False, is_deletabl
             if remove_from_disk:
                 op_description = op_description + " and purged from disk"
             if info_only:
-                print("The following metadata files attached to associations of Dataset '%s' will be %s (without 'info_only' mode):" % (dataset.id, op_description))
+                log.info("The following metadata files attached to associations of Dataset '%s' will be %s (without 'info_only' mode):" % (dataset.id, op_description))
             else:
-                print("The following metadata files attached to associations of Dataset '%s' have been %s:" % (dataset.id, op_description))
+                log.info("The following metadata files attached to associations of Dataset '%s' have been %s:" % (dataset.id, op_description))
                 if remove_from_disk:
                     try:
-                        print("Removing disk file ", metadata_file.file_name)
+                        log.info("Removing disk file ", metadata_file.file_name)
                         os.unlink(metadata_file.file_name)
                     except Exception as e:
-                        print("Error, exception: %s caught attempting to purge metadata file %s\n" % (str(e), metadata_file.file_name))
+                        log.info("Error, exception: %s caught attempting to purge metadata file %s\n" % (str(e), metadata_file.file_name))
                     metadata_file.purged = True
                     app.sa_session.add(metadata_file)
                     app.sa_session.flush()
                 metadata_file.deleted = True
                 app.sa_session.add(metadata_file)
                 app.sa_session.flush()
-            print("%s" % metadata_file.file_name)
+            log.info("%s" % metadata_file.file_name)
         if not info_only:
-            print("Deleting dataset id", dataset.id)
+            log.info("Deleting dataset id", dataset.id)
             dataset.deleted = True
             app.sa_session.add(dataset)
             app.sa_session.flush()
         else:
-            print("Dataset %i will be deleted (without 'info_only' mode)" % (dataset.id))
+            log.info("Dataset %i will be deleted (without 'info_only' mode)" % (dataset.id))
 
 
 def _purge_dataset(app, dataset, remove_from_disk, info_only=False):
@@ -462,7 +462,7 @@ def _purge_dataset(app, dataset, remove_from_disk, info_only=False):
                     # Remove files from disk and update the database
                     if remove_from_disk:
                         # TODO: should permissions on the dataset be deleted here?
-                        print("Removing disk, file ", dataset.file_name)
+                        log.info("Removing disk, file ", dataset.file_name)
                         os.unlink(dataset.file_name)
                         # Remove associated extra files from disk if they exist
                         if dataset.extra_files_path and os.path.exists(dataset.extra_files_path):
@@ -476,32 +476,32 @@ def _purge_dataset(app, dataset, remove_from_disk, info_only=False):
                         for user in usage_users:
                             user.adjust_total_disk_usage(-dataset.get_total_size())
                             app.sa_session.add(user)
-                    print("Purging dataset id", dataset.id)
+                    log.info("Purging dataset id", dataset.id)
                     dataset.purged = True
                     app.sa_session.add(dataset)
                     app.sa_session.flush()
                 else:
-                    print("Dataset %i will be purged (without 'info_only' mode)" % (dataset.id))
+                    log.info("Dataset %i will be purged (without 'info_only' mode)" % (dataset.id))
             else:
-                print("This dataset (%i) is not purgable, the file (%s) will not be removed.\n" % (dataset.id, dataset.file_name))
+                log.info("This dataset (%i) is not purgable, the file (%s) will not be removed.\n" % (dataset.id, dataset.file_name))
         except OSError as exc:
-            print("Error, dataset file has already been removed: %s" % str(exc))
-            print("Purging dataset id", dataset.id)
+            log.error("Error, dataset file has already been removed: %s" % str(exc))
+            log.error("Purging dataset id", dataset.id)
             dataset.purged = True
             app.sa_session.add(dataset)
             app.sa_session.flush()
         except ObjectNotFound:
-            print("Dataset %i cannot be found in the object store" % dataset.id)
+            log.error("Dataset %i cannot be found in the object store" % dataset.id)
         except Exception as exc:
-            print("Error attempting to purge data file: ", dataset.file_name, " error: ", str(exc))
+            log.error("Error attempting to purge data file: ", dataset.file_name, " error: ", str(exc))
     else:
-        print("Error: '%s' has not previously been deleted, so it cannot be purged\n" % dataset.file_name)
+        log.info("Error: '%s' has not previously been deleted, so it cannot be purged\n" % dataset.file_name)
 
 
 def _purge_folder(folder, app, remove_from_disk, info_only=False):
     """Purges a folder and its contents, recursively"""
     for ld in folder.datasets:
-        print("Deleting library dataset id ", ld.id)
+        log.info("Deleting library dataset id ", ld.id)
         ld.deleted = True
         for ldda in [ld.library_dataset_dataset_association] + ld.expired_datasets:
             _purge_dataset_instance(ldda, app, remove_from_disk, info_only=info_only)  # mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable
@@ -509,7 +509,7 @@ def _purge_folder(folder, app, remove_from_disk, info_only=False):
         _purge_folder(sub_folder, app, remove_from_disk, info_only=info_only)
     if not info_only:
         # TODO: should the folder permissions be deleted here?
-        print("Purging folder id ", folder.id)
+        log.info("Purging folder id ", folder.id)
         folder.purged = True
         app.sa_session.add(folder)
         app.sa_session.flush()
diff --git a/scripts/manage_db.py b/scripts/manage_db.py
index c697f6263d8..d0211bc1ef6 100644
--- a/scripts/manage_db.py
+++ b/scripts/manage_db.py
@@ -13,7 +13,7 @@ from galaxy.model.orm.scripts import get_config
 
 def invoke_migrate_main():
     # Migrate has its own args, so cannot use argparse
-    config = get_config(sys.argv, use_argparse=False)
+    config = get_config(sys.argv, use_argparse=False, cwd=os.getcwd())
     db_url = config['db_url']
     repo = config['repo']
 
diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
index 7608c3c0de2..a778dcd0f52 100644
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -343,6 +343,20 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase):
         # Make sure the positions have been updated.
         map(tweak_step, updated_workflow_content['steps'].items())
 
+    def test_update_tags(self):
+        workflow_object = self.workflow_populator.load_workflow(name="test_import")
+        upload_response = self.__test_upload(workflow=workflow_object)
+        workflow = upload_response.json()
+        workflow['tags'] = ['a_tag', 'b_tag']
+        update_response = self._update_workflow(workflow['id'], workflow).json()
+        assert update_response['tags'] == ['a_tag', 'b_tag']
+        del workflow['tags']
+        update_response = self._update_workflow(workflow['id'], workflow).json()
+        assert update_response['tags'] == ['a_tag', 'b_tag']
+        workflow['tags'] = []
+        update_response = self._update_workflow(workflow['id'], workflow).json()
+        assert update_response['tags'] == []
+
     def test_update_no_tool_id(self):
         workflow_object = self.workflow_populator.load_workflow(name="test_import")
         upload_response = self.__test_upload(workflow=workflow_object)
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
new file mode 100644
index 00000000000..256f9d7a1f8
--- /dev/null
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -0,0 +1,41 @@
+import xml.etree.ElementTree as ET
+
+import pytest
+
+from galaxy.tool_util.lint import LintContext
+from galaxy.tool_util.linters import inputs
+
+
+NO_SECTIONS_XML = """
+<tool name="BWA Mapper" id="bwa" version="1.0.1" is_multi_byte="true" display_interface="true" require_login="true" hidden="true">
+    <description>The BWA Mapper</description>
+    <version_command interpreter="python">bwa.py --version</version_command>
+</tool>
+"""
+
+NO_WHEN_IN_CONDITIONAL_XML = """
+<tool name="BWA Mapper" id="bwa" version="1.0.1" is_multi_byte="true" display_interface="true" require_login="true" hidden="true">
+    <description>The BWA Mapper</description>
+    <version_command interpreter="python">bwa.py --version</version_command>
+    <inputs>
+        <conditional name="labels">
+            <param name="label_select" type="select" label="Points to label">
+                <option value="none" selected="True">None</option>
+            </param>
+        </conditional>
+    </inputs>
+</tool>
+"""
+
+TESTS = [
+    (NO_SECTIONS_XML, inputs.lint_inputs, lambda x: 'Found no input parameters.' in x.warn_messages),
+    (NO_WHEN_IN_CONDITIONAL_XML, inputs.lint_inputs, lambda x: 'No <when /> block found for select option \'none\' inside conditional \'labels\'' in x.warn_messages),
+]
+
+
+@pytest.mark.parametrize('tool_xml,lint_func,assert_func', TESTS, ids=['Lint no sections', 'lint no when'])
+def test_tool_xml(tool_xml, lint_func, assert_func):
+    lint_ctx = LintContext('all')
+    tree = ET.ElementTree(element=ET.fromstring(tool_xml))
+    lint_ctx.lint(name="test_lint", lint_func=lint_func, lint_target=tree)
+    assert assert_func(lint_ctx)
diff --git a/test/unit/tool_util/test_tool_loader.py b/test/unit/tool_util/test_tool_loader.py
index ce644a510ef..ceedfd51f32 100644
--- a/test/unit/tool_util/test_tool_loader.py
+++ b/test/unit/tool_util/test_tool_loader.py
@@ -62,8 +62,19 @@ def test_loader():
     <expand macro="inputs">
         <input name="first_input" />
     </expand>
+    <expand macro="inputs">
+        <input name="second_input" />
+    </expand>
+    <expand macro="inputs">
+        <input name="third_input" />
+    </expand>
     <macros>
         <macro name="inputs">
+            <expand macro="foo">
+                <yield />
+            </expand>
+        </macro>
+        <macro name="foo">
             <inputs>
                 <yield />
             </inputs>
@@ -71,7 +82,9 @@ def test_loader():
     </macros>
 </tool>''')
         xml = tool_dir.load()
-        assert xml.find("inputs").find("input").get("name") == "first_input"
+        assert xml.findall("inputs")[0].find("input").get("name") == "first_input"
+        assert xml.findall("inputs")[1].find("input").get("name") == "second_input"
+        assert xml.findall("inputs")[2].find("input").get("name") == "third_input"
 
     # Test recursive macro applications.
     with TestToolDirectory() as tool_dir:
@@ -227,6 +240,8 @@ def test_loader():
         tool_dir.write('''
 <tool>
     <expand macro="inputs" bar="hello" />
+    <expand macro="inputs" bar="my awesome" />
+    <expand macro="inputs" bar="doggo" />
     <macros>
         <xml name="inputs" tokens="bar" token_quote="$$">
             <inputs type="the type is $$BAR$$" />
@@ -236,8 +251,10 @@ def test_loader():
 ''')
         xml = tool_dir.load()
         input_els = xml.findall("inputs")
-        assert len(input_els) == 1
+        assert len(input_els) == 3
         assert input_els[0].attrib["type"] == "the type is hello"
+        assert input_els[1].attrib["type"] == "the type is my awesome"
+        assert input_els[2].attrib["type"] == "the type is doggo"
 
     # Test macros XML macros with @ expansions in text
     with TestToolDirectory() as tool_dir:
@@ -259,3 +276,27 @@ def test_loader():
         assert input_els[0].text == "hello"
         assert input_els[1].text == "world"
         assert input_els[2].text == "the_default"
+
+    # Test macros XML macros with @ expansions and recursive
+    with TestToolDirectory() as tool_dir:
+        tool_dir.write('''
+<tool>
+    <expand macro="inputs" foo="hello" />
+    <expand macro="inputs" foo="world" />
+    <expand macro="inputs" />
+    <macros>
+        <xml name="inputs" token_foo="the_default">
+            <expand macro="real_inputs"><cow>@FOO@</cow></expand>
+        </xml>
+        <xml name="real_inputs">
+            <inputs><yield /></inputs>
+        </xml>
+    </macros>
+</tool>
+''')
+        xml = tool_dir.load()
+        input_els = xml.findall("inputs")
+        assert len(input_els) == 3
+        assert input_els[0].find("cow").text == "hello"
+        assert input_els[1].find("cow").text == "world"
+        assert input_els[2].find("cow").text == "the_default"